Contacts of the strand formed by residues 94 - 102 (chain B) in PDB entry 3Q3G
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 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS* 3.7 31.9 - - + -
41B GLN 3.4 16.2 - - - +
42B ARG* 4.0 4.3 - - - +
43B PRO* 4.6 4.9 - - - -
92B ASP 3.2 3.7 + - - +
93B THR* 1.3 76.1 - - - +
95B VAL* 1.3 62.9 + - - +
96B TYR* 3.6 14.6 - - + -
119B THR* 3.8 1.7 - - - -
120B VAL 2.9 30.1 + - - +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A EDO 6.6 0.2 - - - -
39B VAL 3.9 0.9 - - - +
40B LYS* 3.7 1.2 - - - -
41B GLN* 2.8 42.4 + - + +
94B ALA* 1.3 74.3 - - - +
96B TYR* 1.3 62.2 + - - +
97B TYR* 3.6 38.8 + - + +
117B GLY* 4.0 7.4 - - - -
118B THR 3.4 4.5 - - - +
119B THR* 4.0 14.8 - - + +
606B EDO 3.8 31.2 - - - +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 2.8 21.3 + - - -
22B LEU* 3.7 20.2 - - + -
38B TRP* 4.5 3.6 - - + -
39B VAL 3.5 1.8 - - - +
40B LYS* 3.6 33.7 + - + -
50B ILE* 3.6 28.9 - - + -
66B PHE* 5.6 0.8 - + - -
83B LEU* 3.8 10.8 - - + -
85B LEU* 3.6 20.3 - - + +
92B ASP* 2.6 45.7 + - - +
94B ALA* 3.6 15.5 - - + -
95B VAL* 1.3 72.5 - - - +
97B TYR* 1.3 62.3 + - - +
117B GLY* 3.4 0.9 - - - -
118B THR 2.9 20.1 + - - +
120B VAL* 3.6 28.9 - - + -
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 3.3 17.8 + - - -
48A GLN 3.7 8.3 + - - -
49A SER* 3.4 22.2 - - - -
50A PRO* 4.1 7.9 - - + -
618A EDO 4.3 4.5 + - - -
8B GLN* 3.6 1.8 - - - -
38B TRP* 3.4 10.1 - - - -
39B VAL* 2.8 42.0 + - + +
41B GLN* 3.4 31.6 + - + -
47B LEU* 4.5 4.3 - - + -
95B VAL* 3.6 22.1 - - + +
96B TYR* 1.3 74.7 - - - +
98B CYS* 1.3 61.3 + - - +
114B TRP* 3.8 30.5 - + + -
115B GLY 3.5 17.3 - - - -
116B GLN 3.7 4.0 - - - -
117B GLY* 3.6 19.5 - - - -
606B EDO 4.2 6.6 + - - -
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Residues in contact with CYS 98 (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 LEU* 3.7 10.9 - - - +
8B GLN* 3.2 25.4 + - - -
24B CYS* 2.0 55.2 - - + -
36B MET* 4.6 4.7 - - + -
37B GLN 3.1 10.8 - - - +
38B TRP* 3.9 14.4 - - + -
97B TYR* 1.3 76.0 - - - +
99B ALA* 1.3 60.1 + - - +
114B TRP* 3.5 1.6 - - - -
115B GLY 2.8 26.2 + - - -
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Residues in contact with ALA 99 (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 LEU* 3.9 4.0 - - - -
36B MET* 3.6 5.0 - - - +
37B GLN* 2.6 38.1 + - + +
39B VAL* 5.0 2.2 - - + -
98B CYS* 1.3 75.8 - - - +
100B SER* 1.3 58.9 + - - +
111B MET* 3.8 30.5 - - + -
113B TYR 3.1 13.5 - - - +
114B TRP* 3.9 20.0 - - + -
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Residues in contact with SER 100 (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 LEU* 3.9 1.9 - - - +
29B PHE* 3.9 8.1 - - - -
34B ILE* 3.4 35.7 - - - +
35B TYR 3.4 4.3 - - - -
36B MET* 4.4 3.1 - - - -
37B GLN* 4.6 0.7 - - - -
99B ALA* 1.3 74.6 - - - +
101B GLU* 1.3 59.6 + - - +
111B MET* 3.3 5.2 - - - -
112B ASP* 3.1 26.3 + - - +
113B TYR* 2.9 39.6 + - - +
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Residues in contact with GLU 101 (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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97A TYR* 5.0 0.3 - - - +
100A TYR* 4.5 0.9 + - - -
102A LEU* 4.3 8.7 - - - +
34B ILE* 3.7 3.0 - - - +
35B TYR* 2.9 47.8 + - + +
37B GLN* 3.2 27.2 + - + +
100B SER* 1.3 70.9 - - - +
102B GLY* 1.3 63.3 + - - +
103B HIS* 4.3 3.1 + - - -
108B GLY* 3.6 3.6 - - - -
109B TYR* 3.2 37.8 + - + +
110B ALA 3.4 13.4 - - - +
111B MET* 4.8 2.6 - - + +
208E ARG* 2.9 40.0 + - - -
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Residues in contact with GLY 102 (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 ILE* 3.9 15.9 - - - +
100B SER 3.8 0.4 - - - -
101B GLU* 1.3 78.2 - - - +
103B HIS* 1.3 65.9 + - - -
104B TYR* 3.6 25.9 - - - -
108B GLY 4.9 0.9 - - - -
109B TYR* 3.3 21.9 + - - +
110B ALA 4.1 1.4 + - - -
112B ASP* 3.3 13.4 + - - -
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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