Contacts of the strand formed by residues 19 - 26 (chain Y) in PDB entry 5GGV
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 ALA 19 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Y VAL* 4.0 11.0 - - + -
12Y LEU 5.0 0.4 - - - -
13Y ALA* 4.0 9.6 - - + +
17Y GLY 4.2 0.6 - - - -
18Y ILE* 1.3 76.2 - - - +
20Y SER* 1.3 62.0 + - - +
21Y PHE* 5.1 2.1 - - - -
79Y LEU 4.0 0.3 - - - +
80Y THR* 3.4 1.6 - - - +
81Y ILE* 2.7 40.2 + - + +
84Y LEU* 3.7 22.2 - - + -
114Y ILE* 4.0 25.6 - - + -
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Residues in contact with SER 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y VAL* 3.6 19.0 - - - +
18Y ILE* 4.8 2.9 - - - +
19Y ALA* 1.3 75.5 - - - +
21Y PHE* 1.3 66.8 + - - +
78Y ASN* 4.3 10.9 + - - -
79Y LEU 3.1 9.0 - - - -
80Y THR* 2.8 26.8 + - - +
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Residues in contact with PHE 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y GLN* 3.5 22.9 - - + -
8Y PRO* 3.6 22.2 - - + -
11Y VAL* 3.9 5.8 - - + -
19Y ALA 5.1 0.7 - - - -
20Y SER* 1.3 79.8 - - - +
22Y VAL* 1.3 71.9 + - - +
23Y CYS* 4.7 0.4 - - + -
38Y VAL* 4.6 10.3 - - + -
78Y ASN* 3.7 6.9 + - - -
79Y LEU* 2.8 64.1 + - + +
81Y ILE* 4.1 23.3 - - + -
92Y TYR* 4.6 12.1 - - + -
94Y CYS* 4.7 5.4 - - + -
112Y THR* 3.8 15.5 - - + -
114Y ILE* 4.1 20.6 - - + -
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Residues in contact with VAL 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y ALA 3.7 0.5 - - - +
7Y GLN* 3.4 10.4 - - - +
8Y PRO* 3.3 25.1 - - + +
21Y PHE* 1.3 76.0 - - - +
23Y CYS* 1.3 71.8 + - - +
24Y GLU* 4.1 15.0 - - + +
76Y GLN* 4.0 20.4 - - - +
77Y VAL 3.3 8.7 - - - +
78Y ASN* 3.6 23.3 - - + +
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Residues in contact with CYS 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y VAL* 3.6 17.9 - - - -
6Y ALA 3.5 3.6 - - - -
7Y GLN* 4.6 0.9 - - + -
21Y PHE* 3.9 3.1 + - + -
22Y VAL* 1.3 75.2 - - - +
24Y GLU* 1.3 56.4 + - - +
25Y TYR* 4.1 5.1 - - - -
36Y VAL* 5.5 0.9 - - - -
76Y GLN* 3.2 2.4 - - - -
77Y VAL* 2.7 44.8 + - + +
79Y LEU* 4.2 10.8 - - + -
94Y CYS* 2.0 53.4 - - + -
96Y VAL* 4.1 8.7 - - - -
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Residues in contact with GLU 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y HIS 3.6 0.7 - - - +
5Y VAL* 3.5 1.3 - - - +
6Y ALA* 2.9 52.8 + - + +
22Y VAL* 4.2 12.5 - - + +
23Y CYS* 1.3 75.5 - - - +
25Y TYR* 1.3 62.7 + - - +
75Y ASN 4.4 0.2 - - - +
76Y GLN* 3.6 28.2 - - + +
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Residues in contact with TYR 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y MET* 4.8 6.3 - - + -
4Y HIS 3.1 11.7 - - - +
5Y VAL* 4.0 14.1 - - + -
23Y CYS* 4.1 9.6 - - - -
24Y GLU* 1.3 78.9 - - - +
26Y ALA* 1.3 60.8 + - - +
27Y SER* 4.6 12.1 - - - -
34Y VAL* 5.0 2.5 - - + -
36Y VAL* 4.6 2.1 - - + +
54Y TYR* 2.2 41.9 + - - -
74Y GLY 4.3 0.7 + - - -
75Y ASN* 2.8 71.7 + - + +
76Y GLN* 3.9 8.4 + - - -
77Y VAL* 4.4 12.2 - - + +
96Y VAL* 3.7 41.1 - - + -
98Y LEU* 5.4 3.1 - - + -
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Residues in contact with ALA 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ALA 4.7 1.9 - - - +
3Y MET* 3.3 30.2 - - - +
4Y HIS* 3.1 21.7 + - + +
25Y TYR* 1.3 70.0 - - - +
27Y SER* 1.3 60.6 + - - +
75Y ASN* 5.2 0.4 - - - +
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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