Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 4CMM
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 GLY 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.2 9.2 - - - -
85A ASP 3.6 1.0 + - - -
86A ALA* 1.3 75.5 - - - +
88A THR* 1.3 58.3 + - - -
89A TYR* 3.6 9.1 - - - -
111A GLU* 3.3 14.8 + - - +
112A LEU 2.8 33.9 + - - -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.5 3.3 - - - +
41A GLY* 2.8 34.9 + - - +
87A GLY* 1.3 70.0 - - - -
89A TYR* 1.3 61.8 + - - +
90A TYR* 3.5 33.4 + - + +
108A ALA 5.3 0.9 - - - +
109A GLY* 4.0 3.6 - - - -
110A THR 3.4 22.0 - - - +
111A GLU* 2.6 26.7 + - - +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 2.8 24.9 + - - -
23A LEU* 3.6 20.6 - - + -
38A TRP* 3.7 17.0 - + + -
39A PHE 3.3 13.7 - - - +
40A ARG* 3.5 21.3 + - + -
49A ILE* 3.7 31.2 - - + +
78A ILE* 3.9 18.3 - - + +
85A ASP* 2.6 41.7 + - - +
87A GLY 3.6 17.3 - - - -
88A THR* 1.3 73.6 - - - +
90A TYR* 1.3 57.4 + - - +
109A GLY* 3.2 2.6 - - - -
110A THR 2.8 24.4 + - - +
112A LEU* 3.8 20.6 - - + +
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.5 2.0 - - - -
37A GLN 3.7 1.4 - - - +
38A TRP* 3.3 8.3 - - - -
39A PHE* 2.9 33.6 + - + +
41A GLY* 3.4 36.1 - - - +
42A ALA* 4.0 15.9 - - + +
46A ARG* 6.0 0.4 - - - +
88A THR* 3.5 33.4 + - + +
89A TYR* 1.3 75.6 - - - +
91A CYS* 1.3 58.9 + - - +
92A VAL* 3.8 18.5 + - + +
106A SER* 3.9 7.0 - - - +
107A GLY 3.7 11.0 - - - -
108A ALA 3.8 9.7 + - - -
109A GLY* 3.5 27.6 - - - -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.3 8.4 - - + +
8A GLN* 3.0 16.0 + - + +
25A CYS* 2.0 54.3 - - + -
36A ILE* 3.5 25.4 - - - -
37A GLN 3.7 3.6 - - - -
38A TRP* 3.8 18.1 - - + -
74A PHE* 4.3 1.3 - - - -
90A TYR* 1.3 69.0 - - - +
92A VAL* 1.3 58.9 + - - +
106A SER* 3.6 0.5 - - - -
107A GLY 2.8 26.3 + - - -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 5.3 0.2 - - - -
36A ILE* 3.2 6.2 - - - -
37A GLN 2.8 40.4 + - - +
39A PHE* 3.7 25.8 - - + -
46A ARG* 4.1 8.3 - - - +
90A TYR* 3.8 13.9 - - + +
91A CYS* 1.3 78.7 - - - +
93A LYS* 1.3 62.4 - - - +
94A PHE* 3.6 20.3 - - + -
103A GLU* 3.5 38.1 - - + +
105A LYS 3.6 5.4 - - - +
106A SER* 3.7 15.7 - - - +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.7 20.4 - - + -
6A VAL* 3.9 15.1 - - + +
29A SER 5.4 1.5 + - - +
30A LEU* 3.7 5.1 + - - +
31A ILE 4.7 0.2 - - - -
32A PRO* 2.8 38.4 + - - -
34A GLY 2.7 19.8 + - - +
35A PRO 3.5 8.5 - - - +
36A ILE* 3.8 19.3 - - + -
91A CYS 4.4 0.4 + - - -
92A VAL* 1.3 73.5 - - - +
94A PHE* 1.3 71.4 + - - +
103A GLU* 3.7 3.1 - - - -
104A PHE* 2.8 37.7 + - + -
105A LYS 2.7 23.1 + - - +
102B THR* 3.0 20.8 + - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.1 24.0 - - - -
35A PRO* 2.9 24.3 + - + +
37A GLN* 3.0 32.8 - - + -
39A PHE* 3.7 14.1 - + - -
46A ARG* 3.4 29.8 - - - -
92A VAL* 3.6 26.2 - - + -
93A LYS* 1.3 84.4 - - - +
95A ARG* 1.3 64.3 + - - +
101A ASP* 4.1 20.6 - - + -
102A VAL 3.3 8.3 - - - +
103A GLU* 3.5 27.4 - - + -
104A PHE* 4.0 4.5 - - - +
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.5 39.8 - - + +
33A VAL 3.6 6.5 - - - +
94A PHE* 1.3 73.9 - - - +
96A LYS* 1.3 66.7 + - - +
101A ASP* 3.4 5.0 - - - +
102A VAL* 2.8 41.5 + - + +
104A PHE* 3.7 33.2 - - + +
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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