Contacts of the strand formed by residues 34 - 39 (chain C) in PDB entry 4LOU
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.1 17.3 - - + -
22C CYS* 4.9 0.7 - - - -
27C PHE* 4.9 2.5 - - - -
29C TYR* 3.7 43.3 - - + +
32C TYR* 4.1 6.7 - - - +
33C TRP* 1.3 84.2 - - - +
35C SER* 1.3 61.0 + - - +
50C GLU* 3.3 4.5 - - - +
51C ILE* 2.9 35.3 + - + +
70C ILE* 5.7 0.7 - - - +
72C ARG* 3.9 10.3 - - - +
79C LEU* 3.4 24.7 - - + -
96C CYS* 3.8 25.1 - - - -
97C ALA 3.4 16.8 - - - +
98C ARG* 3.9 15.3 - - + -
99C LEU* 4.7 0.9 - - - -
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C MET* 1.3 76.8 - - - +
36C TRP* 1.3 64.2 + - - +
37C VAL 4.2 0.2 - - - -
47C TRP* 2.9 22.7 + - - -
49C GLY 2.4 26.5 + - - -
50C GLU* 3.9 1.3 - - - +
70C ILE* 6.4 0.4 - - - -
79C LEU* 4.2 3.3 - - - +
96C CYS* 3.5 4.3 - - - -
97C ALA* 2.5 44.0 + - - -
99C LEU* 4.0 24.5 - - - -
108C PHE* 4.1 9.6 - - - -
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Residues in contact with TRP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLU* 4.3 9.4 - - + -
20C LEU* 4.0 21.3 - - + -
21C SER 4.3 1.6 - - - -
22C CYS* 3.8 27.8 - - + -
35C SER* 1.3 82.7 + - - +
37C VAL* 1.3 65.5 + - - +
47C TRP* 3.9 0.3 - - - -
48C ILE* 2.9 43.3 + - + +
49C GLY 3.1 7.4 + - - +
70C ILE* 3.9 29.2 - - + -
79C LEU* 3.5 35.1 - - + +
80C TYR 3.4 16.4 + - - -
81C LEU* 3.5 32.3 - - + +
94C TYR* 4.4 13.0 - - + -
95C TYR 3.3 22.7 - - - -
96C CYS* 4.1 14.1 - - + -
115C THR* 5.7 0.2 - - - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 4.8 0.4 - - - +
36C TRP* 1.3 81.6 - - - +
38C ARG* 1.3 61.2 + - - +
45C LEU* 4.1 13.2 - - + -
46C LYS 3.0 31.4 - - - +
47C TRP* 4.1 7.2 - - + -
48C ILE* 4.3 1.6 - - - +
94C TYR* 4.9 0.9 - - - -
95C TYR* 2.7 36.3 + - - +
97C ALA* 5.2 2.0 - - + -
108C PHE* 3.5 37.0 - - + -
111C TRP* 3.9 27.4 - - + -
97D PHE* 4.1 4.9 - - + -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 1.3 75.1 - - - +
39C GLN* 1.3 62.0 + - - +
40C ALA* 4.4 1.5 + - - +
44C GLY 4.0 0.7 - - - +
45C LEU* 3.8 1.3 - - - -
46C LYS* 2.8 45.3 + - + +
48C ILE* 3.9 17.2 - - + +
68C PHE* 3.8 22.7 - - - -
89C GLU* 2.9 40.7 + - - +
90C ASP* 2.8 21.6 + - - +
92C ALA* 4.0 12.3 - - + -
93C LEU 3.2 10.8 - - - +
94C TYR* 2.6 59.1 + - + +
95C TYR* 5.2 1.1 - - - -
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 1.3 74.6 - - - +
40C ALA* 1.3 70.1 + - - +
41C PRO* 3.7 1.0 - - - +
43C LYS 3.3 20.3 + - - +
44C GLY 4.1 6.7 - - - +
45C LEU* 4.1 15.6 - - + +
92C ALA* 3.4 3.8 - - - -
93C LEU* 2.7 45.2 + - + +
95C TYR* 3.8 13.3 + - + -
37D GLN* 3.0 30.8 + - - -
86D TYR* 3.0 31.3 + - - -
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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