Contacts of the strand formed by residues 11 - 17 (chain b) in PDB entry 5GJQ
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 b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7b VAL* 3.6 1.7 - - - -
8b TYR* 2.8 42.9 + - - +
9b LYS 3.5 0.4 + - - -
10b ASP* 1.3 82.6 - - - +
12b ILE* 1.3 66.0 + - - +
103b VAL* 4.4 3.8 - - - -
108b PRO* 3.7 17.8 - - - +
178b ILE 3.3 8.1 - - - -
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Residues in contact with ILE 12 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6b VAL 3.3 12.6 - - - +
7b VAL* 4.3 5.6 - - + -
8b TYR* 3.2 3.2 - - - -
11b GLY* 1.3 79.3 - - - +
13b VAL* 1.3 67.1 + - - +
14b LEU* 4.0 28.9 - - + -
101b GLY* 4.1 2.7 - - - -
102b GLY 3.3 23.8 - - - +
108b PRO* 4.1 7.0 - - + -
109b HIS 3.1 39.5 - - - +
110b LEU* 4.0 9.4 - - + +
176b CYS 3.6 2.1 - - - +
177b VAL* 3.6 1.2 - - - -
178b ILE* 2.9 49.4 + - + +
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Residues in contact with VAL 13 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5b GLY* 3.3 2.9 - - - -
6b VAL* 2.9 41.9 + - + +
8b TYR* 3.8 23.6 - - + -
12b ILE* 1.3 78.1 - - - +
14b LEU* 1.3 70.7 + - - +
148b GLU 4.8 0.9 - - - +
151b ALA* 3.9 16.2 - - + -
152b LYS* 4.2 22.9 - - + -
155b VAL* 3.7 26.6 - - + +
175b LEU* 4.2 9.2 - - + -
176b CYS 3.5 5.4 - - - +
177b VAL* 4.6 9.4 - - + -
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Residues in contact with LEU 14 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4b ALA 3.5 1.1 - - - -
5b GLY* 3.8 14.1 - - - -
12b ILE* 4.0 9.6 - - + -
13b VAL* 1.3 76.8 - - - +
15b GLY* 1.3 58.8 + - - +
34b ILE* 4.5 6.1 - - + -
42b TYR* 3.5 45.1 - - + +
43b CYS 4.3 0.2 - - - +
44b CYS* 3.7 21.1 - - - +
99b VAL* 3.7 28.9 - - + +
101b GLY* 4.7 4.9 - - - +
110b LEU* 4.0 11.9 - - + -
155b VAL* 4.4 0.4 - - - -
175b LEU* 3.3 8.7 - - - +
176b CYS* 2.9 42.5 + - + +
178b ILE* 4.4 8.3 - - + -
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Residues in contact with GLY 15 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3b ILE* 3.3 5.4 - - - +
4b ALA 2.8 30.7 + - - +
14b LEU* 1.3 77.2 - - - +
16b ALA* 1.3 66.4 + - - +
34b ILE* 4.2 3.1 - - - -
44b CYS* 3.9 2.9 - - - -
155b VAL* 3.9 16.3 - - - +
159b ILE* 3.7 7.4 - - - -
174b ASP 3.1 10.1 - - - -
175b LEU* 4.0 0.7 - - - -
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Residues in contact with ALA 16 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2b THR 3.4 9.0 - - - -
3b ILE* 3.9 17.5 - - + -
15b GLY* 1.3 76.5 - - - +
17b ASP* 1.3 69.0 + - - +
33b LYS* 4.1 8.3 - - + +
34b ILE* 3.8 23.6 - - + -
44b CYS* 5.1 0.2 - - - -
159b ILE* 3.7 10.2 - - - +
173b ILE* 3.4 4.0 - - - -
174b ASP* 2.9 33.7 + - + +
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Residues in contact with ASP 17 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2b THR* 2.5 49.3 + - - +
16b ALA* 1.3 77.8 - - - +
18b THR* 1.3 65.6 + - - +
19b ARG* 3.1 14.4 + - - +
31b CYS 4.1 0.9 - - - +
33b LYS* 2.9 44.5 + - - +
159b ILE* 3.8 3.5 - - + +
163b ILE* 3.9 17.0 - - + -
169b SER* 3.6 12.2 - - - -
170b GLY 3.3 21.6 + - - +
172b ASN 3.4 10.3 - - - +
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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