Contacts of the strand formed by residues 94 - 102 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H LYS* 3.9 15.9 - - + -
41H GLN 3.5 21.3 - - - +
42H ARG* 3.9 9.4 - - + +
43H PRO* 4.6 5.4 - - - -
92H ASP 3.2 3.5 + - - +
93H THR* 1.3 76.5 - - - +
95H VAL* 1.3 63.2 + - - +
96H TYR* 3.6 20.9 - - + +
119H THR* 3.8 2.8 - - - +
120H VAL 2.9 29.9 + - - +
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H VAL 3.9 0.5 - - - +
40H LYS* 3.7 0.9 - - - -
41H GLN* 2.8 43.4 + - + +
94H ALA* 1.3 74.8 - - - +
96H TYR* 1.3 60.9 + - - +
97H TYR* 3.6 36.6 + - + +
116H GLN 5.2 0.9 - - - +
117H GLY* 4.0 17.3 - - - -
118H THR 3.4 5.6 - - - +
119H THR* 4.0 23.3 - - + +
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN* 2.8 25.8 + - - -
22H LEU* 3.7 20.4 - - + -
38H TRP* 4.5 3.8 - - + -
39H VAL 3.5 2.0 - - - +
40H LYS* 3.7 34.8 + - + -
50H ILE* 3.6 28.7 - - + -
66H PHE* 5.6 0.6 - + - -
83H LEU* 3.8 9.9 - - + -
85H LEU* 3.6 21.1 - - + +
92H ASP* 2.6 45.0 + - - +
94H ALA* 3.6 19.7 - - + -
95H VAL* 1.3 70.6 - - - +
97H TYR* 1.3 56.2 + - - +
117H GLY* 3.4 0.2 - - - -
118H THR 2.9 20.2 + - - +
120H VAL* 3.7 24.2 - - + -
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Residues in contact with TYR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLN* 3.2 18.0 + - - -
47F GLY 5.9 0.2 - - - -
48F GLN 3.7 8.3 + - - -
49F SER* 3.4 22.6 - - - -
50F PRO* 3.9 10.8 - - + -
8H GLN* 3.6 1.8 - - - -
38H TRP* 3.4 10.2 - - - -
39H VAL* 2.8 41.5 + - - +
41H GLN* 3.3 32.3 + - + -
47H LEU* 4.5 4.7 - - + -
95H VAL* 3.6 21.9 - - + +
96H TYR* 1.3 74.6 - - - +
98H CYS* 1.3 60.2 + - - +
114H TRP* 3.8 25.4 - + + -
115H GLY 3.5 17.9 - - - -
116H GLN 3.7 5.0 + - - -
117H GLY* 3.6 18.6 - - - -
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Residues in contact with CYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 4.0 11.0 - - - -
8H GLN* 3.2 24.5 + - - -
24H CYS* 2.0 54.7 - - + -
36H MET* 4.6 4.3 - - + -
37H GLN 3.3 11.2 - - - +
38H TRP* 3.9 14.4 - - + -
97H TYR* 1.3 76.5 - - - +
99H ALA* 1.3 59.7 + - - +
114H TRP* 3.5 1.7 - - - -
115H GLY 2.8 26.2 + - - -
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Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 3.9 3.6 - - - -
36H MET* 3.6 4.2 - - - +
37H GLN* 2.6 38.4 + - + +
39H VAL* 5.0 1.6 - - + -
97H TYR 4.2 0.2 + - - -
98H CYS* 1.3 75.8 - - - +
100H SER* 1.3 58.8 + - - +
111H MET* 3.8 31.0 - - + -
113H TYR 3.1 13.2 - - - +
114H TRP* 3.9 21.1 - - + -
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Residues in contact with SER 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 3.9 3.7 - - - +
29H PHE* 3.6 10.4 - - - -
34H ILE* 3.7 29.6 - - - -
35H TYR 3.4 3.1 - - - -
36H MET* 4.2 5.8 - - - -
99H ALA* 1.3 74.7 - - - +
101H GLU* 1.3 58.2 + - - +
111H MET* 3.5 3.8 - - - -
112H ASP* 3.1 27.2 + - - +
113H TYR* 2.9 26.0 + - - +
1000H PEG 3.2 16.8 + - - -
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Residues in contact with GLU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TYR* 5.0 0.3 - - - +
100F TYR* 4.7 1.2 + - - -
102F LEU* 4.3 11.4 - - - +
34H ILE* 3.7 2.4 - - - +
35H TYR* 2.9 47.7 + - + +
37H GLN* 3.5 26.8 + - + +
99H ALA 4.2 0.4 + - - -
100H SER* 1.3 69.9 - - - +
102H GLY* 1.3 63.5 + - - +
103H HIS* 4.3 2.9 + - - -
108H GLY* 3.6 2.8 - - - -
109H TYR* 3.2 37.8 + - + +
110H ALA 3.4 14.5 - - - +
111H MET* 4.4 3.0 - - + +
208I ARG* 2.8 39.4 + - - -
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Residues in contact with GLY 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ILE* 3.6 6.5 - - - -
100H SER 3.8 0.6 + - - -
101H GLU* 1.3 78.3 - - - +
103H HIS* 1.3 65.0 + - - -
104H TYR* 3.6 17.9 - - - -
108H GLY 4.9 1.0 - - - -
109H TYR* 3.3 21.8 + - - +
110H ALA 4.2 1.4 + - - -
112H ASP* 3.3 12.9 + - - -
1000H PEG 3.5 18.6 + - - -
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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