Contacts of the strand formed by residues 95 - 104 (chain B) in PDB entry 4MXV
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 LEU 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LYS* 4.9 15.7 - - - +
93B SER 3.7 1.5 + - - +
94B PRO* 1.3 71.1 - - - +
96B TYR* 1.3 72.0 + - - +
97B LEU* 3.5 12.7 + - + -
120B MET* 3.5 6.7 - - - -
121B VAL* 2.9 45.4 + - + +
129B TRP* 3.8 21.5 - - + -
153B GLY* 5.2 4.0 - - - -
156B HIS* 3.3 39.5 - - + +
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Residues in contact with TYR 96 (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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94B PRO 3.7 4.1 + - - +
95B LEU* 1.3 80.3 - - - +
97B LEU* 1.3 69.8 + - - +
98B ALA* 3.5 24.5 - - + +
118B GLN* 2.9 43.5 + - + +
119B LYS 4.0 6.3 - - - -
120B MET* 4.2 27.6 - - + -
152B ASP* 3.7 33.4 - - + +
153B GLY 4.2 0.7 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.9 31.4 - - + -
95B LEU* 3.5 28.7 + - + +
96B TYR* 1.3 80.8 - - - +
98B ALA* 1.3 66.7 + - - +
118B GLN* 3.5 2.9 - - - -
119B LYS* 3.0 41.1 + - + +
121B VAL* 4.0 11.2 - - + -
129B TRP* 3.7 29.8 - - + -
131B HIS* 4.0 20.0 - - + -
133B MET* 5.1 1.3 - - - -
152B ASP 3.3 11.4 - - - +
153B GLY* 4.2 9.9 - - - -
156B HIS* 4.8 1.6 - - + -
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Residues in contact with ALA 98 (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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81B PHE* 3.7 3.7 - - - -
96B TYR* 3.5 21.5 - - + +
97B LEU* 1.3 79.3 - - - +
99B HIS* 1.3 66.9 + - - +
117B SER 3.3 13.7 - - - +
118B GLN* 4.7 0.7 - - + -
133B MET* 3.8 3.8 - - - +
150B HIS 5.8 0.2 - - - +
151B THR* 3.5 4.4 - - - +
152B ASP* 3.0 49.4 + - + +
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.4 4.7 - - + -
45B TRP* 4.5 2.0 - + - -
77B SER* 2.9 31.3 + - - -
78B GLN 4.8 0.2 - - - -
79B VAL* 3.4 42.2 - - + +
98B ALA* 1.3 78.1 - - - +
100B GLU* 1.3 64.4 + - - +
101B VAL* 5.0 0.4 - - + +
117B SER 3.1 28.2 + - - +
133B MET* 3.4 16.8 - - + +
135B HIS* 4.0 15.0 + - - -
149B THR* 3.6 29.9 - - - +
150B HIS 3.3 7.1 + - - -
151B THR* 2.8 26.1 + - + +
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Residues in contact with GLU 100 (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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99B HIS* 1.3 78.4 - - - +
101B VAL* 1.3 67.5 + - - +
102B GLN* 2.8 40.2 + - + +
113B PRO* 3.3 30.9 - - + +
115B LEU 3.1 11.7 - - - +
116B SER* 4.9 6.6 - - - +
135B HIS* 5.7 0.2 - - - -
149B THR* 3.1 28.3 - - - -
150B HIS* 3.0 24.4 + - + +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.9 24.2 - - + -
77B SER* 3.6 31.9 - - - +
99B HIS* 5.0 0.9 - - - +
100B GLU* 1.3 71.9 - - - +
102B GLN* 1.3 66.5 + - - +
113B PRO* 3.9 1.9 - - - +
114B LEU* 2.9 37.7 + - + +
115B LEU* 2.9 33.6 + - + -
135B HIS* 5.3 2.4 + - + +
147B LEU* 5.0 2.0 - - + -
148B SER 3.5 4.3 - - - +
149B THR* 3.7 11.7 - - + -
166B PHE* 3.9 14.6 - - + -
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Residues in contact with GLN 102 (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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100B GLU* 2.8 44.8 + - + +
101B VAL* 1.3 74.9 - - - +
103B LEU* 1.3 64.0 + - - +
104B PHE 4.1 0.2 - - - -
111B HIS* 3.8 36.4 + - + +
112B VAL 3.6 8.7 - - - +
114B LEU* 4.5 4.3 - - - -
147B LEU* 3.3 10.0 - - - +
148B SER* 2.7 53.6 + - - +
149B THR 4.9 0.3 - - - -
150B HIS* 4.1 23.2 + - - +
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Residues in contact with LEU 103 (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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51A ARG* 3.2 34.3 - - - +
102B GLN* 1.3 75.7 - - - +
104B PHE* 1.3 75.5 + - - +
105B SER* 3.6 1.0 + - - -
111B HIS* 3.7 1.4 - - - -
112B VAL* 3.0 42.6 + - + +
114B LEU* 4.1 13.0 - - + +
141B LEU* 3.8 20.6 - - + -
145B ASP* 3.9 31.9 - - + +
146B GLN 3.4 12.8 - - - +
147B LEU* 3.9 11.0 - - + -
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Residues in contact with PHE 104 (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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102B GLN 4.1 0.8 - - - -
103B LEU* 1.3 87.8 - - - +
105B SER* 1.3 79.3 + - - +
106B SER* 4.9 3.8 - - - -
110B PHE* 3.2 35.2 - + + -
111B HIS* 4.1 18.1 - + + +
145B ASP* 4.9 4.2 - - - +
146B GLN* 3.0 61.1 + - + +
148B SER* 5.2 4.3 + - - +
56F GLY* 6.0 2.2 - - - -
57F THR 4.3 15.9 - - - -
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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