Contacts of the strand formed by residues 31 - 37 (chain H) in PDB entry 4NQD
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 SER 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H HIS* 4.5 0.3 - - - +
30H ASN* 1.3 75.6 - - - +
32H MET* 1.3 64.4 + - - +
33H TYR* 3.4 9.0 - - - -
49H SER 3.1 7.0 - - - -
50H ALA* 2.6 13.0 + - - -
93H SER* 3.3 5.9 - - - -
94H SER* 3.1 44.4 + - - +
96H TRP* 3.2 12.3 - - - -
97H THR* 2.5 30.0 + - - -
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Residues in contact with MET 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H CYS* 3.8 28.3 - - - +
25H GLN* 3.7 18.4 - - + +
31H SER* 1.3 79.9 - - - +
33H TYR* 1.3 64.7 + - - +
48H TYR* 3.4 2.8 - - - +
49H SER* 2.8 34.2 + - - +
68H ARG* 3.7 21.3 - - - +
71H LYS 3.7 16.2 - - - +
72H ARG 3.5 27.4 - - - +
74H PHE* 3.7 34.8 - - + -
91H CYS* 4.1 2.0 - - - -
92H ALA 3.4 5.2 - - - +
93H SER* 4.3 9.6 - - - -
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Residues in contact with TYR 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LEU* 6.4 0.9 - - + -
31H SER* 3.4 21.5 - - - -
32H MET* 1.3 74.5 - - - +
34H TRP* 1.3 59.8 + - - +
35H TYR* 3.9 22.7 - + + -
45H LEU* 3.8 18.8 - - + -
47H TYR 3.8 4.7 - - - -
48H TYR* 3.8 25.6 - + + -
74H PHE* 3.9 5.8 - - - -
91H CYS* 3.3 9.9 - - - -
92H ALA* 2.8 45.7 + - + +
94H SER* 2.6 33.0 + - - -
97H THR* 3.4 29.3 - - + +
104H LEU* 3.4 21.9 - - + +
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Residues in contact with TRP 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 3.3 41.1 - - + -
21H LEU* 3.7 34.1 - - + -
22H GLN 4.1 2.0 - - - -
23H CYS* 3.7 20.1 - - + +
33H TYR* 1.3 70.5 - - - +
35H TYR* 1.3 58.2 + - - +
45H LEU* 3.6 2.6 - - - +
46H ILE* 2.8 36.8 + - + +
47H TYR 2.9 16.0 + - - +
66H VAL* 4.2 5.4 - - + -
74H PHE* 3.1 47.1 + + + -
76H LEU* 3.5 47.6 - - + +
89H TYR* 3.7 18.2 - - + -
90H PHE 3.5 15.5 - - - -
91H CYS* 3.7 11.9 - - + -
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Residues in contact with TYR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LEU* 4.0 10.7 + - - +
99G TRP* 3.3 33.9 + + - -
33H TYR* 3.9 29.8 - - + -
34H TRP* 1.3 73.8 - - - +
36H ARG* 1.3 58.2 + - - +
43H LEU* 3.7 26.5 - - + -
44H ARG 3.5 6.5 - - - -
45H LEU* 3.5 42.5 - - + +
46H ILE* 3.7 6.4 - - - +
89H TYR* 3.4 5.9 - - - +
90H PHE* 2.7 44.3 + - + +
92H ALA* 4.6 2.5 - - + -
104H LEU* 3.9 25.8 - - + +
106H PHE* 4.0 17.3 - + - -
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Residues in contact with ARG 36 (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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35H TYR* 1.3 73.1 - - - +
37H GLN* 1.3 59.6 + - - +
38H ASP* 2.8 39.2 + - - +
42H GLY 4.8 0.9 - - - +
43H LEU* 3.9 4.5 - - - -
44H ARG* 3.0 54.7 + - + +
46H ILE* 3.8 14.3 - - + +
60H VAL* 4.4 16.8 - - + +
64H TYR* 3.2 29.2 + - - -
84H SER* 2.8 30.9 + - - -
85H GLN* 3.8 5.8 - - - +
86H THR 3.7 8.3 + - - -
87H SER* 3.5 14.7 + - - +
88H VAL 3.4 4.0 - - - -
89H TYR* 3.9 9.4 - - + -
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Residues in contact with GLN 37 (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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37G GLN* 2.9 43.8 + - - +
43G PRO* 5.3 0.6 - - - +
87G LEU* 4.4 14.6 - - - +
36H ARG* 1.3 72.5 - - - +
38H ASP* 1.3 68.7 + - - +
39H PRO* 4.7 1.0 - - - +
41H MET 5.2 6.9 + - - +
42H GLY 5.8 0.4 - - - -
43H LEU* 3.7 29.5 - - + +
87H SER* 3.1 12.1 + - - -
88H VAL* 2.8 33.3 + - + +
90H PHE* 3.4 14.6 - - + -
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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
------------------------------------------------------------
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