Contacts of the strand formed by residues 25 - 30 (chain P) in PDB entry 5GAD
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 ARG 25 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B C 2.7 40.5 + - - -
9B G 3.3 9.7 + - - -
15P ARG* 3.5 31.5 + - - +
18P LEU* 3.7 28.5 - - + -
19P GLN* 6.4 1.8 - - - -
23P ALA 3.6 6.2 + - - +
24P THR* 1.3 75.3 - - - +
26P LEU* 1.3 60.6 + - - +
27P VAL* 3.6 20.3 + - + +
39P VAL* 3.7 1.2 - - - -
40P ILE* 2.9 51.6 + - + +
41P ALA 5.4 1.7 + - - +
44P GLY* 4.6 10.5 + - - -
90P VAL* 4.7 2.7 - - - -
91P SER 3.8 4.3 - - - +
93P ASP* 3.1 28.0 + - + +
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Residues in contact with LEU 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P THR 4.3 0.2 + - - -
25P ARG* 1.3 71.8 - - - +
27P VAL* 1.3 60.4 + - - +
28P VAL* 3.7 0.6 + - + +
37P ALA* 3.7 26.0 - - + -
38P GLN 3.2 23.1 - - - +
39P VAL* 3.9 18.8 - - + +
78P VAL* 4.7 9.0 - - + -
90P VAL* 4.3 12.5 - - + +
91P SER 2.9 15.6 + - - +
92P PHE* 3.6 33.0 - - + -
93P ASP* 2.9 30.2 + - - +
106P LEU* 4.9 7.0 - - + -
110P ALA* 5.0 4.3 - - + -
115P LEU* 4.4 19.5 - - + -
117P PHE* 4.5 5.8 - - + -
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Residues in contact with VAL 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B G 4.4 8.3 - - - +
8B C 3.8 15.3 - - - -
15P ARG* 3.8 6.5 - - - +
25P ARG* 3.6 35.6 + - + +
26P LEU* 1.3 72.9 - - - +
28P VAL* 1.3 67.2 + - - +
29P HIS* 4.0 1.7 + - + +
37P ALA* 3.4 2.1 - - - +
38P GLN* 2.9 39.3 + - + +
40P ILE* 3.6 29.6 - - + -
93P ASP* 3.7 8.3 - - + +
95P SER* 3.5 19.7 - - - +
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Residues in contact with VAL 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P LEU* 3.7 1.1 + - + -
27P VAL* 1.3 76.0 - - - +
29P HIS* 1.3 64.5 + - - +
30P ARG 4.3 1.2 + - - +
35P ILE* 4.2 23.6 - - + -
36P TYR 3.3 13.0 - - - +
37P ALA* 4.3 2.9 - - + +
92P PHE* 3.8 22.4 - - + -
93P ASP 3.0 19.2 + - - +
94P ARG* 3.8 15.5 - - - +
95P SER* 3.4 22.3 + - - -
97P PHE* 4.3 2.7 - - + -
103P VAL* 4.3 15.9 - - + -
106P LEU* 4.5 17.9 - - + -
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Residues in contact with HIS 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B G 4.7 2.6 + - - -
7B G 3.4 56.3 + - - +
8B C 5.8 0.2 - - - +
28B C 5.6 3.0 + - - -
29B A 5.5 1.2 + - - -
4P LYS* 5.5 0.2 - - - -
7P ARG* 3.7 34.1 + - - -
27P VAL* 4.0 3.4 + - + -
28P VAL* 1.3 76.2 - - - +
30P ARG* 1.3 86.9 + - - +
31P THR* 3.5 8.7 + - - -
35P ILE* 3.6 0.9 - - - +
36P TYR* 2.9 72.4 + + + +
95P SER* 6.0 0.2 - - - -
97P PHE* 4.4 2.5 - + - -
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Residues in contact with ARG 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B A 5.1 1.4 + - - -
48B U 3.0 41.8 + - - -
49B C 2.9 29.3 + - - -
28P VAL* 5.5 0.4 - - + -
29P HIS* 1.3 88.4 + - - +
31P THR* 1.3 73.9 + - - +
32P PRO* 5.9 3.2 - - - +
34P HIS 4.1 1.1 - - - -
35P ILE* 3.8 22.2 - - + -
97P PHE* 3.4 50.3 - - + -
102P ARG* 3.6 38.0 - - - +
103P VAL* 4.3 13.8 - - + +
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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