Contacts of the helix formed by residues 160 - 180 (chain I) in PDB entry 1XFB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 160 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I THR* 4.3 3.7 - - - +
122I GLU* 2.6 31.4 + - - -
157I ARG 4.9 5.8 - - - -
158I THR 2.2 17.3 + - - -
159I PRO* 1.3 69.3 - - - +
161I ALA* 1.3 69.4 + - - +
162I LEU* 3.9 8.4 + - - +
163I ALA* 2.8 23.6 + - - +
164I ILE* 2.8 14.3 + - - +
3J HIS* 6.1 4.7 - - - -
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Residues in contact with ALA 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159I PRO 4.1 0.8 + - - -
160I SER* 1.3 70.5 - - - +
162I LEU* 1.3 52.7 + - - +
164I ILE* 3.3 8.0 + - - +
165I LEU* 2.7 41.3 + - + +
161K ALA* 4.8 18.6 - - + -
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Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 4.0 15.5 - - + -
117I ALA 4.5 4.0 - - - +
119I THR* 3.9 13.5 - - + -
160I SER* 2.9 9.2 + - - +
161I ALA* 1.3 79.3 - - - +
163I ALA* 1.3 55.7 + - - +
165I LEU* 3.1 11.0 + - + +
166I GLU* 2.7 38.9 + - + +
219J ASP* 3.4 32.3 - - + +
220J HIS* 3.8 40.2 - - + +
221J HIS* 3.7 27.4 - - + +
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Residues in contact with ALA 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 3.8 17.9 - - + +
122I GLU* 2.9 33.9 - - + +
123I THR 4.7 0.7 - - - +
152I LEU* 3.8 12.5 - - + +
159I PRO 4.6 0.7 - - - -
160I SER* 2.8 18.4 + - - +
162I LEU* 1.3 75.9 - - - +
164I ILE* 1.3 52.4 + - - +
166I GLU 2.6 21.1 - - - +
167I ASN* 2.6 24.3 + - - +
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Residues in contact with ILE 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I LEU* 4.6 7.0 - - + -
159I PRO* 3.6 35.0 - - + +
160I SER 2.8 20.0 + - - +
161I ALA* 3.8 6.3 - - - +
163I ALA* 1.3 68.1 - - - +
165I LEU* 1.3 59.3 + - - +
166I GLU 2.5 18.5 - - - +
167I ASN* 5.0 0.4 - - - -
168I ALA* 3.0 20.9 + - + +
205I VAL* 6.0 0.7 - - + -
208I LYS* 4.7 11.2 - - + +
209I VAL* 4.4 28.7 - - + +
212I ALA* 3.5 29.4 - - + -
3L HIS* 6.5 0.2 - - + -
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Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I ALA* 2.7 24.2 + - + +
162I LEU* 3.4 9.0 - - + +
164I ILE* 1.3 72.4 - - - +
166I GLU* 1.3 89.2 + - + +
168I ALA* 3.6 3.1 - - - +
169I ASN* 3.1 25.1 + - + +
212I ALA* 6.1 0.7 - - - -
169J ASN* 3.6 25.1 - - - +
219J ASP* 3.8 31.9 - - + +
220J HIS* 4.3 5.4 - - - +
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Residues in contact with GLU 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 4.4 11.4 - - + -
124I THR* 3.0 35.1 + - - +
125I THR 5.4 0.5 - - - +
162I LEU* 2.7 24.9 + - + +
163I ALA 2.6 13.9 - - - +
164I ILE 2.5 20.1 - - - +
165I LEU* 1.3 81.3 - - + +
167I ASN* 1.3 59.5 + - - +
169I ASN* 3.9 4.8 - - - +
170I VAL* 3.3 16.1 - - - +
128J LEU* 5.6 1.0 - - - +
169J ASN* 2.9 29.7 + - - -
173J ARG* 3.3 27.5 - - - +
220J HIS* 4.0 4.3 - - + -
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Residues in contact with ASN 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 4.7 0.6 - - - +
123I THR 3.0 23.0 + - - +
124I THR* 3.5 18.5 - - - +
150I CYS* 3.3 31.6 - - + +
151I VAL 4.2 2.9 + - - -
152I LEU* 3.5 21.8 - - + +
163I ALA* 2.6 24.9 + - - +
164I ILE* 4.2 1.1 - - - +
166I GLU* 1.3 81.1 + - - +
168I ALA* 1.3 55.2 + - - +
169I ASN 3.0 0.4 - - - -
170I VAL* 3.1 14.8 - - - +
171I LEU* 2.7 43.0 + - + +
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Residues in contact with ALA 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ILE* 3.0 19.2 + - + +
165I LEU* 3.6 3.6 - - - +
166I GLU 2.8 7.5 + - - -
167I ASN* 1.3 74.0 - - - +
169I ASN* 1.3 62.5 + - - +
171I LEU* 3.6 11.8 + - - +
172I ALA* 3.2 16.6 + - - +
212I ALA* 4.1 11.2 - - + +
213I VAL* 4.0 33.1 - - + +
216I ALA* 3.4 16.0 - - + +
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Residues in contact with ASN 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I LEU* 3.1 20.1 + - + +
166I GLU* 4.3 9.8 + - - +
167I ASN 3.0 0.4 - - - -
168I ALA* 1.3 76.4 - - - +
170I VAL* 1.3 65.9 + - - +
172I ALA* 3.1 7.0 + - - +
173I ARG* 2.9 24.7 + - - +
216I ALA* 4.3 5.1 - - - +
220I HIS* 2.8 26.4 + - - -
165J LEU* 3.5 15.9 - - - +
166J GLU* 3.1 25.5 + - - -
169J ASN* 3.6 20.8 - - - +
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Residues in contact with VAL 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I THR* 3.5 9.9 - - - +
125I THR 3.5 10.1 - - - +
128I LEU* 4.3 15.0 - - + -
148I TRP* 3.3 37.9 - - + +
150I CYS* 4.6 1.1 - - - -
166I GLU* 3.3 24.0 - - - +
167I ASN* 3.0 28.2 + - - +
169I ASN* 1.3 76.3 - - - +
171I LEU* 1.3 65.1 + - - +
173I ARG* 3.1 7.5 + - - +
174I TYR* 2.9 23.3 + - - +
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Residues in contact with LEU 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I TRP* 3.6 27.8 - - + +
150I CYS* 3.6 22.9 - - + -
167I ASN* 2.7 25.0 + - + +
168I ALA 3.7 3.8 - - - +
170I VAL* 1.3 74.2 - - - +
172I ALA* 1.3 53.0 + - - +
174I TYR* 3.2 9.3 + - + -
175I ALA* 2.8 36.6 + - - +
187I VAL* 3.5 36.1 - - + -
188I GLU 4.0 6.1 - - - +
189I PRO* 3.8 26.2 - - + -
213I VAL* 4.2 15.0 - - + -
217I LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I ALA 3.2 10.3 + - - +
169I ASN 3.1 6.4 + - - +
171I LEU* 1.3 79.7 - - - +
173I ARG* 1.3 62.0 + - - +
176I SER* 2.9 25.8 + - - -
216I ALA* 3.8 18.2 - - + +
217I LEU* 3.7 16.3 - - + +
220I HIS* 3.4 35.2 - - + +
222I VAL* 3.6 4.0 - - - +
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Residues in contact with ARG 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I LEU* 3.7 28.1 - - + +
169I ASN* 2.9 17.4 + - - +
170I VAL* 3.1 8.9 + - - +
172I ALA* 1.3 76.1 - - - +
174I TYR* 1.3 64.2 + - - +
176I SER* 3.1 11.0 + - - -
177I ILE* 3.0 59.9 + - - +
220I HIS* 3.8 19.6 + - + -
114J VAL* 4.3 7.5 - - - +
115J PRO 3.7 20.8 + - - -
116J LEU* 3.9 19.0 - - - +
117J ALA* 5.1 2.8 - - - +
124J THR* 3.5 19.6 - - - +
166J GLU* 3.2 30.2 + - - +
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Residues in contact with TYR 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I VAL* 3.6 16.8 - - + -
128I LEU* 3.7 9.1 - - + +
131I LEU* 4.0 7.2 - - + -
146I ALA* 3.0 25.3 + - + -
147I LYS* 3.3 1.2 - - - -
148I TRP* 3.3 59.5 - + + -
170I VAL 2.9 11.5 + - - +
171I LEU* 3.4 16.4 - - + +
173I ARG* 1.3 76.4 - - - +
175I ALA* 1.3 69.3 + - + +
177I ILE* 3.2 4.0 + - - +
178I CYS* 3.0 46.7 + - - -
185I PRO* 3.5 15.2 - - + +
186I ILE 2.9 31.4 + - - -
187I VAL* 4.4 7.4 - - + -
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Residues in contact with ALA 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I LEU 2.8 19.5 + - - +
172I ALA 3.7 0.2 - - - +
174I TYR* 1.3 75.3 - - + +
176I SER* 1.3 64.1 + - - +
178I CYS* 3.2 4.0 + - - +
179I GLN* 3.1 27.6 + - - +
185I PRO* 3.8 27.8 - - + -
187I VAL* 4.5 5.6 - - + -
217I LEU* 3.9 11.4 - - + -
222I VAL* 3.6 23.1 - - + -
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Residues in contact with SER 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I ALA 2.9 18.3 + - - -
173I ARG* 3.1 12.4 + - - -
175I ALA* 1.3 75.9 - - - +
177I ILE* 1.3 64.1 + - - +
179I GLN* 3.5 6.7 + - - +
180I GLN* 3.3 23.1 + - - +
220I HIS* 3.7 24.8 + - - -
221I HIS 5.5 0.7 + - - -
222I VAL* 3.7 8.4 - - - +
117J ALA* 3.5 25.1 + - - +
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Residues in contact with ILE 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I LEU* 3.9 28.7 - - + +
131I LEU* 4.0 21.1 - - + +
132I SER* 3.5 41.7 - - - +
135I CYS* 4.8 0.2 - - - -
173I ARG* 3.0 44.7 + - - +
174I TYR 3.6 5.2 - - - +
176I SER* 1.3 71.9 - - - +
178I CYS* 1.3 67.2 + - - +
180I GLN* 3.1 27.5 - - - +
181I ASN* 3.1 9.3 + - - +
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Residues in contact with CYS 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I VAL* 5.1 0.7 - - - -
131I LEU* 4.8 1.3 - - - -
135I CYS* 4.0 25.4 - - - -
146I ALA* 4.1 13.0 - - - -
174I TYR* 3.0 47.6 + - - -
175I ALA 3.6 7.0 - - - +
177I ILE* 1.3 77.4 - - - +
179I GLN* 1.3 58.2 + - - +
181I ASN* 2.8 20.8 + - - +
183I ILE* 3.1 33.7 + - + +
185I PRO* 3.8 11.0 - - + -
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Residues in contact with GLN 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.5 21.2 - - + +
12I GLN* 5.4 1.4 + - - +
16I LEU* 3.8 20.7 - - + +
175I ALA 3.1 14.2 + - - +
176I SER* 3.9 5.3 - - - +
178I CYS* 1.3 72.1 - - - +
180I GLN* 1.3 58.4 + - - +
181I ASN 2.9 10.1 + - - -
182I GLY* 3.1 11.6 + - - -
183I ILE 3.8 4.9 - - - +
185I PRO* 3.8 12.6 - - + -
221I HIS 4.8 1.0 - - - +
222I VAL* 3.7 11.7 - - - +
223I TYR* 2.8 59.4 + - - +
226I GLY* 3.0 24.0 + - - -
227I THR* 3.5 4.6 - - - +
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Residues in contact with GLN 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ALA 5.3 4.3 - - - +
8I LEU* 4.1 12.5 - - + +
12I GLN* 4.8 10.0 + - - +
132I SER* 3.5 18.1 + - - -
176I SER 3.3 9.3 + - - +
177I ILE* 3.1 27.1 - - - +
179I GLN* 1.3 77.7 - - - +
181I ASN* 1.3 63.1 + - - +
182I GLY 3.5 1.1 + - - -
115J PRO* 5.1 14.9 + - - +
117J ALA* 3.5 32.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il