Contacts of the helix formed by residues 154 - 163 (chain I) in PDB entry 6N1H
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 THR 154 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152I GLU* 2.8 16.7 + - - +
153I PRO* 1.3 73.8 - - + +
155I ASN* 1.3 56.1 + - - +
156I PRO* 3.3 6.2 - - - +
157I SER* 2.8 43.0 + - - -
158I LYS* 3.5 2.4 + - - +
144J GLU 4.2 4.9 - - - +
147J GLN* 3.0 13.9 - - - +
148J ALA* 2.5 55.6 - - + +
151J ALA* 6.1 0.4 - - + -
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Residues in contact with ASN 155 (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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123I ILE 4.9 0.2 - - - -
126I VAL 3.9 7.6 + - - +
127I THR* 3.4 37.4 + - - +
129I VAL* 3.3 23.4 + - - +
130I GLU* 5.4 2.9 + - - +
153I PRO 3.3 6.0 + - - +
154I THR* 1.3 69.6 - - - +
156I PRO* 1.4 61.2 - - + +
157I SER 3.4 0.2 + - - -
158I LYS* 3.4 21.1 + - - +
159I MET* 3.7 11.6 + - - +
147J GLN* 3.0 25.9 + - - +
164M SER* 4.8 6.6 + - - +
165M PHE* 5.6 2.0 - - - -
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Residues in contact with PRO 156 (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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123I ILE* 3.3 40.0 - - + +
124I ALA* 4.4 10.1 - - - +
126I VAL 5.9 0.4 - - - +
154I THR* 3.7 7.6 - - - +
155I ASN* 1.4 74.4 - - + +
157I SER* 1.3 56.6 + - - +
159I MET* 3.3 2.7 + - - +
160I ARG* 3.1 31.5 + - - +
143J ASP* 4.9 2.2 - - - +
144J GLU* 3.6 33.9 - - + +
147J GLN* 2.4 37.2 - - + +
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Residues in contact with SER 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F ARG* 4.4 11.8 + - - -
151I ALA 5.0 0.4 - - - -
152I GLU* 3.3 31.0 + - - +
154I THR* 2.8 32.5 + - - -
156I PRO* 1.3 71.6 - - - +
158I LYS* 1.3 60.7 + - - +
159I MET 3.3 0.2 - - - -
160I ARG* 3.6 14.3 - - - +
161I LYS* 3.1 26.0 + - - +
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Residues in contact with LYS 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I VAL* 3.8 24.0 - - + +
130I GLU* 5.6 9.6 + - - +
133I LEU* 5.9 1.1 - - + -
149I VAL* 3.3 39.1 - - + +
150I ARG* 4.5 12.1 - - + +
151I ALA* 3.7 20.0 - - - +
153I PRO* 4.5 19.7 + - - +
154I THR 3.5 6.0 + - - +
155I ASN* 3.4 22.0 + - - +
156I PRO 3.2 0.4 - - - -
157I SER* 1.3 78.0 - - - +
159I MET* 1.3 58.2 + - - +
161I LYS* 3.6 0.8 + - - -
162I LEU* 3.1 20.6 + - - +
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Residues in contact with MET 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I LEU* 3.3 31.0 - - + +
123I ILE* 3.8 12.8 - - + +
126I VAL* 3.9 20.4 - - + +
129I VAL* 3.7 35.2 - - + -
132I LEU* 5.8 4.0 - - + -
155I ASN 3.7 6.6 + - - +
156I PRO 3.3 8.8 + - - +
157I SER 3.3 0.2 - - - -
158I LYS* 1.3 76.7 - - - +
160I ARG* 1.3 55.1 + - - +
161I LYS 3.2 0.2 - - - -
162I LEU* 3.0 22.9 + - + +
163I PHE* 2.7 64.2 + - + -
177I LEU* 5.5 6.1 - - + -
181I LEU* 5.6 2.9 - - + -
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Residues in contact with ARG 160 (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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130F GLU* 2.3 51.0 + - - +
131F TRP* 3.6 12.3 - - - +
134F ASP* 1.8 47.8 + - - -
146F TYR* 3.6 5.4 + - - +
150F ARG* 3.5 42.0 + - - +
119I ARG* 4.6 3.5 + - - +
123I ILE* 3.7 28.2 - - + +
156I PRO* 3.1 18.2 + - - +
157I SER* 3.4 13.3 + - - +
158I LYS 3.4 0.4 - - - -
159I MET* 1.3 75.7 - - - +
161I LYS* 1.3 60.9 + - - +
163I PHE* 4.0 3.7 - - - +
164I SER* 3.2 20.6 + - - -
144J GLU* 4.3 13.3 - - - +
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Residues in contact with LYS 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F ARG* 4.9 7.9 - - - +
148I ALA* 3.4 32.3 - - + +
149I VAL* 3.7 17.3 - - + -
152I GLU* 4.1 24.4 + - - +
157I SER 3.1 17.1 + - - +
158I LYS* 4.0 5.8 - - - +
159I MET 3.2 0.2 - - - -
160I ARG* 1.3 75.1 - - - +
162I LEU* 1.3 61.6 + - - +
164I SER* 3.3 18.2 + - - +
165I PHE* 3.2 37.0 - - + -
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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
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129I VAL* 4.7 4.0 - - + -
132I LEU* 5.1 10.8 - - + +
133I LEU* 3.7 28.3 - - + +
136I LEU* 5.8 0.4 - - + -
141I LEU* 4.9 8.7 - - + +
149I VAL* 4.3 7.8 - - + +
158I LYS 3.1 16.9 + - - +
159I MET* 3.0 35.8 + - + +
161I LYS* 1.3 78.0 - - - +
163I PHE* 1.3 69.8 + - + +
164I SER 3.4 0.7 + - - -
165I PHE* 3.4 14.4 + - - +
166I THR* 3.7 7.4 + - - -
169I TRP* 4.3 12.8 - - + -
177I LEU* 3.7 32.8 - - + -
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Residues in contact with PHE 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ASP* 5.3 0.5 - - - +
115I ILE* 3.6 36.1 - - + -
116I ASP* 5.4 2.2 - - - -
119I ARG* 3.7 45.6 + - + +
122I LEU* 3.7 31.0 - - + -
123I ILE* 3.8 25.6 - - + -
159I MET* 2.7 52.8 + - + +
160I ARG 4.0 0.9 - - - +
162I LEU* 1.3 77.7 - - + +
164I SER* 1.3 62.6 + - - +
165I PHE 3.2 1.1 - - - -
166I THR* 3.2 27.2 + - - -
167I PRO* 3.4 11.8 - - - +
169I TRP* 6.3 0.2 - + - -
177I LEU* 5.9 1.3 - - + -
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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