Contacts of the strand formed by residues 11 - 17 (chain H) in PDB entry 3SDI
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 11 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H LYS* 3.6 2.9 - - - +
8H PHE* 2.9 35.7 + - - +
10H ASN* 1.3 80.0 - - - +
12H VAL* 1.3 62.7 + - - +
108H SER* 3.5 25.6 + - - -
178H MET 3.3 11.9 - - - -
179H GLU* 4.4 0.2 - - - -
180H ILE 4.5 0.4 - - - -
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL 3.6 14.8 - - - +
7H LYS* 4.2 7.4 - - + -
8H PHE* 3.3 5.5 - - - -
11H GLY* 1.3 75.0 - - - +
13H VAL* 1.3 68.4 + - - +
102H ALA* 3.7 21.8 - - + -
103H GLY* 3.6 40.6 - - - +
108H SER* 4.5 5.2 - - - +
109H HIS 3.9 7.4 - - - +
110H LEU* 4.0 20.4 - - + -
177H VAL* 4.1 0.2 - - - -
178H MET* 3.0 37.1 + - + +
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Residues in contact with VAL 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H GLY* 3.4 2.9 - - - -
6H VAL* 3.0 56.7 + - + +
8H PHE* 4.4 6.7 - - + -
12H VAL* 1.3 76.5 - - - +
14H ILE* 1.3 71.3 + - - +
151H ALA* 3.9 25.4 - - + +
152H ILE* 4.7 7.4 - - + -
155H ALA* 4.4 12.1 - - + +
175H VAL* 3.5 30.1 - - + -
176H CYS 3.4 7.9 - - - +
177H VAL* 4.4 8.7 - - + -
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Residues in contact with ILE 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 3.3 12.3 - - - +
5H GLY* 4.2 5.6 - - - -
13H VAL* 1.3 78.0 - - - +
15H ALA* 1.3 62.9 + - - +
34H LEU* 4.0 24.4 - - + +
42H TRP* 3.5 33.2 - - + +
43H CYS* 3.8 15.9 - - - +
44H ALA* 5.5 2.5 - - + +
100H ILE* 4.2 11.9 - - + +
102H ALA* 3.3 29.8 - - + +
155H ALA* 5.4 0.2 - - - -
175H VAL* 3.4 4.2 - - - +
176H CYS* 2.8 37.0 + - + +
178H MET* 3.8 11.4 - - + -
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H ILE* 3.4 3.5 - - - +
4H VAL* 2.9 39.3 + - + +
14H ILE* 1.3 75.4 - - - +
16H ALA* 1.3 63.5 + - - +
34H LEU* 4.1 4.8 - - - +
44H ALA* 4.8 0.9 - - - +
155H ALA* 4.2 10.8 - - + +
159H ILE* 3.7 22.0 - - + -
173H VAL* 4.5 1.8 - - + -
174H ASP 3.1 13.5 - - - +
175H VAL* 3.9 15.0 - - + -
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR 3.3 12.1 - - - +
3H ILE* 3.9 13.9 - - + -
15H ALA* 1.3 78.7 - - - +
17H ASP* 1.3 67.7 + - - +
33H LYS* 4.1 12.3 - - + -
34H LEU* 3.6 21.5 - - + +
159H ILE* 3.7 7.5 - - - +
173H VAL* 3.5 4.9 - - - -
174H ASP* 3.0 31.6 + - + +
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Residues in contact with ASP 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H THR* 3.8 0.7 - - - +
2H THR* 2.7 31.2 + - - +
16H ALA* 1.3 78.7 - - - +
18H THR* 1.3 61.9 + - - +
19H ARG* 3.1 20.3 + - - +
31H CYS 4.8 0.2 - - - +
33H LYS* 3.1 40.3 + - - +
159H ILE* 3.7 14.0 - - + +
163H ILE* 4.0 9.2 - - + -
169H SER* 3.4 18.0 - - - -
170H GLY 3.2 23.7 + - - +
172H ASN 3.1 9.6 - - - +
174H ASP* 5.1 0.3 - - - +
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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