Contacts of the strand formed by residues 34 - 42 (chain B) in PDB entry 3A9L
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 MET 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 3.0 11.8 + - - +
33B SER* 1.3 77.8 - - - +
35B ILE* 1.3 77.6 + - - +
36B TYR* 3.4 31.4 - - + +
61B GLY* 3.5 4.3 - - - -
62B SER 2.9 21.7 + - - -
96B HIS* 3.5 8.9 - - - -
98B ASP* 3.6 9.2 - - + -
99B ALA* 4.0 8.3 - - - +
100B VAL* 3.8 17.0 - - + -
122B LEU* 3.4 33.0 - - + -
203B GLU* 3.9 25.6 - - + +
207B TYR* 3.5 21.1 - - + +
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Residues in contact with ILE 35 (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 MET* 1.3 77.5 - - - +
36B TYR* 1.3 69.1 - - - +
37B PHE* 4.2 5.9 + - + -
62B SER 3.5 12.8 - - - +
63B LEU 4.2 0.7 - - - -
64B TYR* 3.8 21.8 - - + -
92B MET* 3.5 42.8 - - + -
93B LEU* 4.1 15.3 - - + -
96B HIS* 3.7 23.3 - - + +
98B ASP 3.5 14.4 + - - +
99B ALA* 3.3 13.5 - - + +
100B VAL 2.9 30.8 + - - +
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Residues in contact with TYR 36 (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 MET* 3.4 21.3 - - + +
35B ILE* 1.3 71.6 - - - +
37B PHE* 1.3 65.5 + - - +
52B ILE* 4.0 10.3 - - + +
55B VAL* 3.7 22.0 - - + -
56B VAL* 4.1 13.9 - - + -
59B THR* 3.4 26.5 - - - +
61B GLY* 4.2 13.0 - - - -
62B SER 3.0 11.8 + - - +
63B LEU* 3.4 2.4 - - - -
64B TYR 3.2 16.8 + - - -
100B VAL* 3.4 24.5 - - + -
102B PHE* 3.5 26.7 - + + -
122B LEU* 5.9 0.3 - - - +
199B ILE* 3.8 16.3 - - + +
203B GLU* 2.5 41.0 + - - +
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Residues in contact with PHE 37 (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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35B ILE* 4.3 11.7 - - + -
36B TYR* 1.3 77.7 - - - +
38B SER* 1.3 68.9 + - - +
39B PRO* 4.0 11.0 - - + -
52B ILE* 3.2 13.9 - - - +
64B TYR* 3.2 36.3 - + + +
84B PHE* 5.8 0.7 - + - -
93B LEU* 3.8 32.3 - - + -
99B ALA* 4.0 3.8 - - + -
100B VAL 3.0 13.2 + - - -
101B SER* 3.1 15.5 - - - -
102B PHE* 3.0 24.8 + - - -
152B ILE* 3.8 28.5 - - + -
153B VAL* 3.7 41.7 - - + -
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Residues in contact with SER 38 (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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37B PHE* 1.3 81.2 - - - +
39B PRO* 1.4 63.7 - - - +
40B HIS* 2.9 20.3 + - - +
41B ALA* 3.4 18.1 + - - -
48B THR* 3.7 6.1 + - - -
52B ILE* 3.5 13.6 - - - +
64B TYR* 3.2 7.5 + - - +
65B LEU* 3.6 3.2 - - - -
66B PHE* 3.0 24.9 + - - +
102B PHE 2.9 23.5 + - - -
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Residues in contact with PRO 39 (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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37B PHE* 4.0 15.4 - - + +
38B SER* 1.4 85.8 - - - +
40B HIS* 1.3 76.7 + - + +
41B ALA 3.7 1.1 - - - -
44B ILE* 4.1 1.0 - - - +
64B TYR* 4.9 0.4 - - + -
66B PHE* 3.4 25.7 - - + +
77B LEU 5.2 0.2 - - - +
81B SER* 4.6 1.6 - - - +
84B PHE* 3.5 48.8 - - + -
101B SER* 4.9 0.7 - - - -
102B PHE 4.5 0.7 - - - +
103B HIS* 3.7 34.8 - - + +
152B ILE* 4.5 8.5 - - + -
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Residues in contact with HIS 40 (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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38B SER* 2.9 8.5 + - - +
39B PRO* 1.3 104.2 - - + +
41B ALA* 1.3 60.8 + - - +
44B ILE* 3.8 12.6 - - + -
45B GLU* 2.7 56.6 + - - +
48B THR* 3.4 1.2 + - - -
66B PHE 3.8 0.7 - - - -
78B HIS* 3.1 22.2 - + - -
79B VAL 2.8 35.0 + - - -
81B SER 4.4 0.7 - - - -
84B PHE* 5.1 0.2 - + - -
103B HIS* 3.3 7.7 + + - -
251B ZN 2.1 33.0 - - - -
261B PO4 3.0 26.2 - - - -
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Residues in contact with ALA 41 (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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38B SER* 4.0 5.4 - - - +
40B HIS* 1.3 80.5 - - - +
42B GLY* 1.3 69.9 + - - +
44B ILE* 3.2 5.4 + - - +
48B THR* 3.2 14.4 - - - +
49B THR* 3.2 13.2 - - - +
65B LEU* 3.7 27.1 - - + -
66B PHE 2.9 13.6 + - - +
67B GLN* 3.7 11.9 - - + -
68B GLY 3.0 15.1 + - - -
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Residues in contact with GLY 42 (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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41B ALA* 1.3 71.2 - - - +
43B GLY* 1.3 59.7 + - - -
44B ILE 3.6 0.3 + - - -
45B GLU 3.7 1.7 - - - +
46B VAL* 3.5 22.0 - - - +
47B GLY 4.3 2.6 + - - -
49B THR* 2.7 26.9 + - - +
50B GLU* 5.6 0.3 - - - +
67B GLN* 3.8 10.3 - - - +
68B GLY 3.6 11.4 - - - -
185B ARG* 4.2 12.8 + - - -
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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