Contacts of the strand formed by residues 109 - 119 (chain B) in PDB entry 3GAX
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 THR 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B TYR* 5.3 2.3 + - - -
103B ALA* 3.4 3.7 - - - +
104B VAL* 3.0 50.9 + - - +
105B PRO* 4.4 0.9 - - - +
107B GLN* 3.6 23.3 + - + +
108B GLY* 1.3 80.7 - - - +
110B MET* 1.3 64.4 + - - +
111B THR* 5.4 6.3 - - - -
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Residues in contact with MET 110 (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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22B GLY 5.7 0.2 - - - +
25B ARG* 4.0 18.4 - - + +
26B ALA* 3.9 20.6 - - - -
29B PHE* 3.5 53.3 - - + -
62B TYR* 6.3 0.2 - - - -
101B ILE* 3.3 24.7 - - + -
102B TYR 3.3 7.0 - - - +
103B ALA* 4.4 9.6 - - + -
108B GLY 4.4 0.4 + - - -
109B THR* 1.3 77.7 - - - +
111B THR* 1.3 67.0 + - - +
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Residues in contact with THR 111 (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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29B PHE* 3.7 8.1 - - - -
101B ILE* 3.5 4.2 - - - +
102B TYR* 2.9 54.3 + - + +
109B THR* 5.4 4.9 - - - -
110B MET* 1.3 82.6 - - - +
112B LEU* 1.3 62.2 + - - +
113B SER* 3.5 2.4 + - - -
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Residues in contact with LEU 112 (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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29B PHE* 3.5 16.0 - - + -
30B ALA* 4.1 27.4 - - + +
33B GLU* 3.9 28.0 - - + +
34B TYR 5.4 0.9 - - - +
99B PHE* 4.4 3.1 - - + -
100B GLN 3.5 8.7 - - - +
101B ILE* 4.1 7.6 - - + -
111B THR* 1.3 71.3 - - - +
113B SER* 1.3 61.4 + - - +
114B LYS 3.4 24.7 - - - +
115B SER* 3.9 20.2 - - - +
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Residues in contact with SER 113 (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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61B ASN* 4.8 0.7 + - - -
100B GLN* 2.9 35.4 + - - +
102B TYR* 3.8 24.8 + - - +
111B THR* 3.5 2.5 + - - -
112B LEU* 1.3 73.9 - - - +
114B LYS* 1.3 69.7 + - - +
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Residues in contact with LYS 114 (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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98B SER 4.5 1.8 - - - +
99B PHE* 3.4 0.7 - - - -
100B GLN* 2.9 57.7 + - + +
112B LEU* 3.4 12.8 - - - +
113B SER* 1.3 89.7 - - - +
115B SER* 1.3 65.5 + - - +
116B THR* 6.0 2.9 - - + -
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Residues in contact with SER 115 (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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30B ALA 5.6 0.2 + - - -
34B TYR* 5.1 6.1 - - - +
98B SER 3.4 6.5 - - - -
99B PHE* 3.2 27.4 - - - -
112B LEU* 3.9 19.3 - - - +
114B LYS* 1.3 79.3 - - - +
116B THR* 1.3 62.4 + - - +
117B CYS* 4.3 5.2 - - - -
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Residues in contact with THR 116 (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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97B CYS* 3.1 2.6 - - - -
98B SER* 2.9 52.6 + - - +
114B LYS* 6.0 3.1 - - + -
115B SER* 1.3 76.4 + - - +
117B CYS* 1.3 64.6 + - - +
118B GLN* 4.5 9.3 + - - +
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Residues in contact with CYS 117 (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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34B TYR* 3.8 31.6 - - + +
95B ALA* 4.5 6.5 - - + -
97B CYS* 2.1 49.6 - - - +
99B PHE* 4.1 9.0 - - - -
115B SER* 4.5 3.4 - - - -
116B THR* 1.3 76.9 + - - +
118B GLN* 1.3 62.1 + - - +
119B ASP* 5.4 0.7 - - - -
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Residues in contact with GLN 118 (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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95B ALA* 3.3 21.9 - - - +
97B CYS 4.9 3.1 - - - +
116B THR* 4.8 9.3 + - - +
117B CYS* 1.3 78.5 - - - +
119B ASP* 1.3 77.3 + - - +
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Residues in contact with ASP 119 (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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93B ARG* 4.4 28.3 + - - +
94B LYS 3.7 10.3 - - - +
95B ALA* 3.7 14.4 - - - +
117B CYS 5.4 0.3 - - - -
118B GLN* 1.3 89.3 + - - +
120B ALA* 1.3 71.3 + - - +
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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