Contacts of the helix formed by residues 157 - 172 (chain A) in PDB entry 2D7I
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 GLY 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASN* 2.9 29.3 + - - -
115A ILE* 4.4 5.6 - - - -
156A GLU* 1.3 79.1 - - - +
158A TRP* 1.3 64.6 + - - -
159A SER 3.6 1.6 - - - -
160A SER* 3.6 10.9 + - - -
161A LEU* 3.1 23.7 + - - +
189A ARG* 6.2 0.4 - - - -
191A HIS* 4.0 5.2 - - - -
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Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.9 2.8 - - - +
119A ASP* 5.6 2.2 - - - +
123A LEU* 5.5 2.7 - - + +
157A GLY* 1.3 72.3 - - - +
159A SER* 1.3 67.2 + - - +
161A LEU* 3.8 2.5 - - + +
162A LEU* 3.0 59.4 + - + +
191A HIS* 3.4 60.0 + - + +
192A LEU* 5.1 2.0 - - + -
195A PRO* 3.9 13.7 - - + -
196A LEU* 3.6 23.8 - - + -
199A TYR* 3.9 33.0 - + + -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.5 3.7 - - - +
118A SER* 2.7 36.0 + - - -
119A ASP* 2.7 30.5 + - - -
121A ILE 5.7 0.2 - - - -
123A LEU* 3.3 22.9 - - - +
157A GLY 3.6 0.2 - - - -
158A TRP* 1.3 83.6 - - - +
160A SER* 1.3 59.8 + - - +
162A LEU 3.2 0.7 + - - -
163A ARG* 2.7 30.8 + - - +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.4 38.7 - - - -
115A ILE* 4.3 1.1 - - - +
118A SER* 3.5 9.6 + - - -
156A GLU* 4.6 2.4 - - - +
157A GLY* 3.3 18.2 + - - -
159A SER* 1.3 79.9 + - - +
161A LEU* 1.3 62.1 + - - +
163A ARG* 3.5 9.1 + - - +
164A THR* 3.1 24.8 + - - -
238A SER 3.5 2.8 - - - +
239A HIS* 4.4 6.2 - - - -
240A CYS 4.9 0.5 - - - +
371A ILE* 4.6 11.7 - - - -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.7 7.6 - - + -
153A PHE* 4.5 21.5 - - + -
156A GLU* 4.7 6.5 - - + -
157A GLY 3.1 19.2 + - - +
158A TRP* 3.8 3.1 - - + +
159A SER 3.2 0.2 - - - -
160A SER* 1.3 75.2 + - - +
162A LEU* 1.3 70.2 + - + +
164A THR* 3.1 14.5 + - - -
165A VAL* 3.2 24.6 + - + +
182A LEU* 5.0 5.8 - - + -
192A LEU* 3.9 27.8 - - + -
196A LEU* 4.0 25.1 - - + -
200A MET* 5.2 0.7 - - + -
238A SER* 3.6 32.5 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.7 23.6 - - + -
158A TRP* 3.0 59.8 + - + +
161A LEU* 1.3 78.9 - - + +
163A ARG* 1.3 59.0 + - - +
165A VAL* 3.4 3.6 + - - +
166A HIS* 2.9 35.6 + - + -
196A LEU* 4.0 15.5 - - + -
199A TYR* 3.5 37.7 - - + +
200A MET* 3.4 24.9 - - + -
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 2.5 45.6 + - - +
121A ILE* 2.8 38.3 + - - +
122A SER 3.3 19.3 + - - -
123A LEU* 3.5 29.5 - - + +
124A ASN 5.8 0.2 - - - -
125A ARG* 4.0 9.6 - - + +
159A SER* 2.7 21.5 + - - +
160A SER* 3.9 11.8 - - - +
161A LEU 3.2 0.2 - - - -
162A LEU* 1.3 69.7 - - - +
164A THR* 1.3 68.0 + - - +
166A HIS* 3.9 0.3 - - - +
167A SER* 3.0 23.9 + - - -
240A CYS 4.2 0.9 - - - +
241A GLU* 3.8 37.7 + - + +
274A PHE* 3.7 13.0 - - - -
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.0 21.5 - - + -
160A SER 3.1 7.6 + - - -
161A LEU* 3.1 10.2 + - - -
163A ARG* 1.3 75.9 - - - +
165A VAL* 1.3 63.8 + - - +
167A SER* 2.6 21.8 + - - +
168A VAL* 3.1 12.6 + - + +
236A LEU* 4.8 3.6 - - + -
237A ASP 3.9 18.8 - - - +
238A SER* 2.9 24.1 + - - -
240A CYS* 3.0 36.7 + - + +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.6 7.0 - - + -
161A LEU* 3.2 18.9 + - + +
162A LEU 3.9 4.9 - - - +
164A THR* 1.3 76.6 - - - +
166A HIS* 1.3 60.1 + - + +
168A VAL* 3.1 7.7 + - - +
169A LEU* 2.8 46.1 + - + +
180A ILE* 4.6 8.7 - - + -
182A LEU* 3.9 26.2 - - + -
200A MET* 4.0 24.7 - - + -
206A VAL* 3.9 20.2 - - + -
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Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.3 32.2 + - + +
124A ASN* 2.6 25.2 + - - +
162A LEU* 2.9 33.0 + - + +
163A ARG 3.9 0.2 - - - +
165A VAL* 1.3 79.0 - - + +
167A SER* 1.3 56.0 + - - +
169A LEU* 2.9 11.7 + - + -
170A ASN* 2.7 42.7 + - - +
199A TYR* 2.9 34.8 + + - -
200A MET* 6.2 0.4 - - + -
203A PHE* 4.4 3.8 - + - -
1B NAG 3.2 31.3 + - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU 4.8 0.8 + - - -
124A ASN* 6.5 0.2 - - - +
163A ARG* 3.0 14.3 + - - -
164A THR* 2.6 20.4 + - - +
166A HIS* 1.3 75.7 - - - +
168A VAL* 1.3 59.9 + - - +
170A ASN* 5.0 0.9 - - - -
171A ARG* 3.0 56.7 + - - +
240A CYS 4.6 0.3 - - - -
241A GLU* 3.6 11.0 - - - -
242A ALA* 3.2 33.1 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.4 34.8 - - + -
151A ILE* 4.8 2.9 - - + -
164A THR* 3.1 17.6 + - + +
165A VAL* 3.5 9.4 - - - +
166A HIS 3.1 0.6 - - - -
167A SER* 1.3 87.1 + - - +
169A LEU* 1.3 60.0 + - - +
172A SER* 2.8 41.5 + - - +
177A VAL* 5.1 1.3 - - + +
180A ILE* 3.9 19.7 - - + -
236A LEU* 3.8 28.5 - - + -
242A ALA* 4.8 4.3 - - + -
246A TRP* 4.8 4.3 - - + -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL* 2.8 34.7 + - + +
166A HIS* 3.5 6.3 - - + +
168A VAL* 1.3 79.7 - - - +
170A ASN* 1.3 70.5 + - - +
171A ARG 3.7 0.2 + - - -
172A SER 3.8 11.8 - - - +
174A PRO* 5.6 1.0 - - - +
180A ILE* 3.3 28.0 - - + -
203A PHE* 3.7 40.4 - - + -
205A SER* 3.4 17.9 - - - +
206A VAL* 4.4 2.0 - - + -
1B NAG 4.1 8.3 - - - +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 5.7 0.7 - - - +
79A ALA* 5.5 7.1 - - - +
124A ASN* 3.1 18.6 + - - +
166A HIS 2.7 23.3 + - - +
167A SER* 5.0 0.4 - - - -
169A LEU* 1.3 75.5 + - - +
171A ARG* 1.3 70.0 + - + +
172A SER 3.6 0.9 - - - -
1B NAG 2.4 50.5 + - - +
2B NAG 5.1 4.9 + - - -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 3.9 19.8 + - - -
124A ASN* 3.6 10.3 + - - +
125A ARG 2.8 29.9 + - - -
126A SER* 3.8 9.7 - - - +
127A LEU* 3.7 18.9 - - - +
167A SER* 3.0 37.3 + - - +
170A ASN* 1.3 87.8 - - + +
172A SER* 1.3 61.3 + - - +
173A PRO* 4.2 4.4 - - - +
241A GLU* 5.1 1.4 + - - +
242A ALA 2.9 26.4 + - - +
243A ASN* 4.1 20.6 - - - +
244A VAL* 4.3 8.3 - - - +
245A ASN* 4.6 9.3 + - - +
246A TRP* 3.5 18.0 + - + -
248A PRO* 5.8 0.2 - - - +
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 2.8 25.8 + - - +
169A LEU 3.8 10.9 - - - +
170A ASN 3.6 0.8 - - - -
171A ARG* 1.3 78.5 - - - +
173A PRO* 1.3 70.1 - - - +
174A PRO* 3.0 10.0 - - - +
177A VAL* 3.7 24.0 - - - +
246A TRP* 3.0 33.2 + - - +
247A LEU* 4.2 4.0 - - - -
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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
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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