Contacts of the strand formed by residues 105 - 117 (chain V) in PDB entry 6GYK
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 VAL 105 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84V GLN* 4.3 31.4 - - + +
85V VAL 3.3 6.1 - - - +
86V THR* 4.2 16.2 - - + +
104V SER* 1.3 82.9 + - - +
106V ILE* 1.3 68.9 + - - +
107V SER* 4.3 2.6 + - - +
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Residues in contact with ILE 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269U ILE* 3.7 19.1 - - + -
270U ASN* 3.5 27.1 - - + +
274U TYR* 4.2 21.8 - - + +
83V CYS 3.8 0.9 - - - +
84V GLN* 3.4 5.0 - - - -
85V VAL* 2.9 47.8 + - + +
87V VAL* 4.0 23.1 - - + -
104V SER* 3.7 17.9 - - - +
105V VAL* 1.3 81.2 - - - +
107V SER* 1.3 66.1 + - - +
108V VAL* 3.8 1.9 + - + +
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Residues in contact with SER 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270U ASN* 3.4 21.8 + - - +
83V CYS 3.9 3.1 - - - -
84V GLN* 4.8 12.5 + - - +
105V VAL* 4.4 3.1 + - - +
106V ILE* 1.3 73.2 - - - +
108V VAL* 1.3 59.7 + - - +
109V ASP* 4.3 7.0 - - - +
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Residues in contact with VAL 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ASN* 4.3 13.2 - - + +
269U ILE* 3.7 36.8 - - + -
270U ASN* 5.2 2.9 - - - +
82V ASN* 3.1 4.9 - - - -
83V CYS* 2.9 46.7 + - - +
85V VAL* 4.0 11.9 - - + -
106V ILE* 4.1 3.4 - - + +
107V SER* 1.3 78.5 - - - +
109V ASP* 1.3 63.6 + - - +
110V LYS 3.4 31.0 - - - +
111V LEU* 3.8 14.1 - - + -
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Residues in contact with ASP 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ASN* 5.4 2.5 - - - +
270U ASN* 5.9 0.2 + - - -
81V LYS* 3.3 12.8 - - - +
82V ASN* 3.0 33.4 + - - +
107V SER* 4.6 5.4 - - - +
108V VAL* 1.3 79.6 + - - +
110V LYS* 1.3 61.2 + - + +
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Residues in contact with LYS 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241U GLU 5.1 0.2 - - - +
242U ASN* 3.3 31.2 + - - +
79V ILE* 4.2 21.5 - - + +
80V VAL 3.4 6.3 - - - +
81V LYS* 3.7 25.7 - - + +
108V VAL* 3.4 4.3 - - - +
109V ASP* 1.3 82.8 - - + +
111V LEU* 1.3 63.5 + - - +
112V ARG* 4.3 23.6 - - - +
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Residues in contact with LEU 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ASN* 3.7 22.7 - - + +
243U LEU 4.3 1.1 - - - +
244U MET* 4.0 24.0 - - + +
267U VAL* 4.4 7.2 - - + -
269U ILE* 4.1 29.2 - - + -
62V VAL* 4.1 16.4 - - + -
78V PHE 3.9 0.3 - - - +
79V ILE* 3.4 4.6 - - - +
80V VAL* 2.9 36.3 + - + +
83V CYS* 3.8 21.5 - - - -
85V VAL* 4.6 0.9 - - + -
108V VAL* 3.8 9.6 - - + -
110V LYS* 1.3 78.2 - - - +
112V ARG* 1.3 73.4 + - - +
113V ILE* 4.2 9.8 + - + +
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Residues in contact with ARG 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ASN 3.4 11.7 + - - +
243U LEU* 3.5 24.8 - - + +
244U MET* 2.8 33.1 + - - +
12V ARG* 5.2 7.9 - - - +
77V THR* 4.4 12.0 - - + +
78V PHE 3.4 8.7 - - - +
79V ILE* 3.5 34.5 - - + +
110V LYS* 4.3 21.9 - - + +
111V LEU* 1.3 75.2 - - - +
113V ILE* 1.3 60.3 + - - +
114V VAL* 4.4 13.7 - - + -
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Residues in contact with ILE 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244U MET* 3.7 45.3 - - + +
246U CYS* 4.6 4.0 - - - -
262U LEU* 4.3 13.0 - - + -
281U VAL* 4.3 26.2 - - + -
62V VAL* 5.2 2.7 - - + -
77V THR* 3.2 6.6 - - - +
78V PHE* 2.9 59.0 + - + +
80V VAL* 4.9 7.2 - - + -
111V LEU* 4.3 15.3 - - + +
112V ARG* 1.3 78.9 - - - +
114V VAL* 1.3 71.3 + - - +
115V ALA* 4.2 2.7 - - + +
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Residues in contact with VAL 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243U LEU* 4.5 8.5 - - + -
244U MET 3.1 12.8 + - - +
245U LEU* 3.8 14.2 - - + +
246U CYS 3.4 21.8 + - - +
9V LEU* 4.7 15.2 - - + +
12V ARG* 4.7 17.9 - - - +
75V VAL* 4.3 19.5 - - + -
76V TRP 3.5 2.7 - - - -
77V THR* 4.2 15.9 - - + +
112V ARG* 4.4 14.1 - - + -
113V ILE* 1.3 80.5 - - - +
115V ALA* 1.3 64.7 + - - +
116V CYS* 5.5 1.8 - - - -
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Residues in contact with ALA 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246U CYS* 3.2 22.2 - - - +
247U LEU* 3.9 3.1 - - - -
248U TYR* 3.7 31.3 - - + +
262U LEU* 4.3 5.4 - - + -
9V LEU* 5.4 0.2 - - - -
75V VAL* 3.5 4.9 - - - +
76V TRP* 2.9 38.6 + - + +
78V PHE* 6.2 1.3 - - + -
113V ILE* 4.2 4.0 - - + -
114V VAL* 1.3 75.0 - - - +
116V CYS* 1.3 64.3 + - - +
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Residues in contact with CYS 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246U CYS 3.6 6.3 + - - -
247U LEU* 3.3 19.2 - - + +
248U TYR* 3.2 26.8 + - - -
7V TYR* 3.9 28.3 - - + -
9V LEU* 3.6 21.8 - - - -
74V ASP 3.4 6.7 - - - +
75V VAL* 3.8 27.6 - - - -
114V VAL* 5.5 2.5 - - - -
115V ALA* 1.3 74.3 - - - +
117V ASN* 1.3 66.6 + - - +
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Residues in contact with ASN 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247U LEU* 4.4 0.9 - - - +
248U TYR* 3.4 27.0 + - - +
7V TYR* 3.1 31.7 + - - +
74V ASP* 3.4 30.5 + - + +
116V CYS* 1.3 76.4 - - - +
118V SER* 1.3 77.5 + - - +
119V LYS* 2.9 46.1 + - - +
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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