Contacts of the strand formed by residues 91 - 99 (chain A) in PDB entry 3G33
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 GLU 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.7 40.0 + - + +
44A VAL 2.9 19.9 - - - +
45A PRO* 4.7 1.6 - - + -
46A ASN* 3.4 9.8 + - - +
86A SER* 4.3 0.5 - - - -
88A THR* 3.0 51.5 + - + +
90A ARG* 1.3 80.1 - - + +
92A ILE* 1.3 61.5 + - - +
93A LYS* 4.7 4.9 + - - +
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Residues in contact with ILE 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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43A ARG* 3.3 1.1 - - - -
44A VAL* 2.4 64.7 + - + +
45A PRO 4.5 5.8 - - - +
46A ASN* 4.0 13.2 - - + +
54A LEU* 4.8 6.5 - - + -
84A ALA* 4.6 3.8 - - + -
85A THR 3.3 28.3 - - - +
86A SER* 3.5 21.3 - - - +
87A ARG 5.1 0.7 - - - +
88A THR 5.6 0.4 - - - +
91A GLU* 1.3 73.8 - - - +
93A LYS* 1.3 60.1 + - - +
94A VAL* 4.1 12.3 - - + -
142D VAL* 3.6 42.2 - - + -
150D TRP* 6.3 0.7 - - + -
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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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41A SER* 5.8 6.1 - - - -
42A VAL 3.5 6.5 - - - +
43A ARG* 4.1 22.5 - - + +
83A CYS 3.9 0.5 - - - +
84A ALA* 3.5 2.6 - - - -
85A THR* 3.0 38.9 + - - +
87A ARG* 3.7 42.5 - - + +
88A THR* 3.6 24.0 + - - +
91A GLU* 4.7 9.7 + - - +
92A ILE* 1.3 73.8 - - - +
94A VAL* 1.3 62.4 + - - +
95A THR* 3.9 5.3 + - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 3.7 1.0 - - - +
41A SER* 3.4 1.8 - - - -
42A VAL* 2.7 50.2 + - + +
44A VAL* 3.4 27.4 - - + -
58A THR* 5.7 1.3 - - + -
62A VAL* 5.4 5.2 - - + -
82A VAL* 3.9 21.3 - - + -
83A CYS 3.4 9.0 - - - +
84A ALA* 4.7 3.1 - - + -
92A ILE* 4.1 9.9 - - + -
93A LYS* 1.3 73.9 - - - +
95A THR* 1.3 65.5 + - - +
96A LEU* 3.9 11.2 + - + -
169A ILE* 6.4 0.2 - - + -
150D TRP* 4.1 27.6 - - + -
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Residues in contact with THR 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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39A LEU* 3.9 33.0 - - + -
40A LYS 3.5 10.3 - - - +
41A SER* 3.3 21.4 + - - +
82A VAL* 3.5 3.8 - - - +
83A CYS* 2.6 53.3 + - + +
93A LYS* 3.9 5.8 + - - +
94A VAL* 1.3 73.1 - - - +
96A LEU* 1.3 63.9 + - - +
97A VAL* 3.6 4.9 + - + +
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Residues in contact with LEU 96 (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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38A ALA 3.4 5.2 - - - +
40A LYS* 2.7 57.1 + - + +
42A VAL* 4.1 21.8 - - + -
62A VAL* 4.6 20.9 - - + -
65A LEU* 5.0 1.6 - - + -
79A LEU* 3.8 22.4 - - + -
81A ASP 4.0 3.8 - - - -
82A VAL* 4.8 3.6 - - + +
94A VAL* 4.0 18.6 - - + +
95A THR* 1.3 72.3 - - - +
97A VAL* 1.3 60.3 + - - +
98A PHE* 3.4 30.6 + - + -
166A LEU* 4.4 15.7 - - + -
169A ILE* 4.8 4.7 - - + -
170A TYR* 4.9 2.7 - - + +
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Residues in contact with VAL 97 (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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11A TYR* 3.7 39.7 - - + +
37A VAL* 3.7 34.5 - - + -
38A ALA 4.0 2.5 - - - -
39A LEU* 3.8 16.6 - - + -
79A LEU* 3.6 2.7 - - - +
80A MET* 2.8 30.3 + - + +
81A ASP* 2.8 32.3 + - + +
83A CYS* 4.4 8.3 - - - -
95A THR* 4.2 7.4 - - + +
96A LEU* 1.3 70.3 - - - +
98A PHE* 1.3 57.3 + - - +
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Residues in contact with PHE 98 (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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37A VAL* 3.5 8.5 - - - +
38A ALA* 2.9 47.2 + - + +
40A LYS* 4.2 30.7 - - + +
65A LEU* 4.5 10.8 - - + -
77A VAL* 3.9 20.4 - - + -
78A ARG 3.5 13.9 - - - -
79A LEU* 3.9 23.1 - - + -
80A MET* 4.1 2.7 - - - -
96A LEU* 3.5 39.7 - - + -
97A VAL* 1.3 75.7 - - - +
99A GLU* 1.3 60.6 + - - +
100A HIS 3.4 0.7 + - - -
162A ALA* 6.3 0.4 - - + -
163A ASP 5.6 6.3 - - - -
164A PHE* 5.4 8.5 - + - -
166A LEU* 4.4 19.7 - - + -
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Residues in contact with GLU 99 (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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36A PHE 5.0 0.9 - - - -
37A VAL* 5.5 0.7 - - - -
38A ALA* 4.8 1.9 - - - +
76A VAL 4.0 3.1 - - - +
77A VAL* 3.4 25.2 - - + +
78A ARG* 2.7 60.2 + - + +
80A MET* 3.9 14.2 - - - +
98A PHE* 1.3 73.3 - - - +
100A HIS* 1.3 68.3 + - - +
101A VAL* 3.9 4.7 + - + +
152A LEU* 5.0 1.9 - - - +
160A LYS* 3.5 30.4 + - - +
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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