Contacts of the helix formed by residues 165 - 170 (chain I) in PDB entry 6NIL
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 165 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TRP* 3.6 9.5 - - - -
104I ASP* 4.3 19.7 - - - -
163I LEU* 3.0 19.7 + - - -
164I PRO* 1.3 74.5 - - - +
166I VAL* 1.3 64.0 + - - +
167I ARG* 4.4 5.5 + - - +
168I LYS* 3.2 33.8 + - - +
169I LEU 3.5 3.5 + - - -
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Residues in contact with VAL 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I TRP* 3.6 24.0 - - + -
66I ILE* 3.7 26.0 - - + -
87I ILE* 4.7 11.9 - - + -
100I PRO* 3.8 23.1 - - + +
103I ALA* 3.8 20.4 - - + -
104I ASP* 3.9 10.1 - - + +
107I ILE* 5.3 6.9 - - + +
164I PRO 4.2 0.9 + - - +
165I SER* 1.3 70.5 - - - +
167I ARG* 1.3 62.7 + - - +
168I LYS 3.3 0.2 - - - -
169I LEU* 3.2 13.3 + - + +
170I THR* 3.1 34.8 + - + +
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Residues in contact with ARG 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I PRO* 4.2 9.4 - - + +
101I ASP* 3.4 30.0 + - - +
104I ASP* 3.3 26.6 + - + +
165I SER* 3.2 3.0 - - - +
166I VAL* 1.3 80.4 - - - +
168I LYS* 1.3 65.7 + - - +
169I LEU 3.4 0.2 + - - -
170I THR* 3.6 10.5 + - - +
171I GLU* 3.2 46.9 + - - +
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Residues in contact with LYS 168 (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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347A ASP* 5.1 9.5 + - - -
17I ARG* 3.5 45.8 + - - +
24I LEU* 6.5 1.1 - - + -
165I SER* 3.2 26.3 + - - +
167I ARG* 1.3 82.4 - - - +
169I LEU* 1.3 63.2 + - - +
171I GLU* 4.2 5.3 + - - +
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Residues in contact with LEU 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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13I VAL* 3.8 24.1 - - + +
17I ARG* 3.5 34.2 - - + +
18I ILE* 4.5 7.2 - - + -
21I TRP* 3.5 50.9 - - + -
66I ILE* 5.6 0.9 - - + -
85I VAL* 3.7 37.9 - - + -
165I SER 3.5 4.2 + - - +
166I VAL* 3.2 19.0 + - + +
167I ARG 3.2 0.4 - - - -
168I LYS* 1.3 82.1 - - - +
170I THR* 1.3 62.1 + - + +
171I GLU 3.1 8.1 + - - +
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Residues in contact with THR 170 (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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63H ASN* 2.6 30.3 + - - +
11I TRP* 4.4 20.3 - - + -
13I VAL* 4.0 8.5 - - - -
85I VAL* 4.0 15.9 - - + -
87I ILE* 6.2 2.5 - - + -
100I PRO* 3.7 28.2 - - + +
166I VAL* 3.1 21.1 + - + +
167I ARG* 3.6 6.8 + - - +
169I LEU* 1.3 88.7 - - + +
171I GLU* 1.3 60.2 + - - +
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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