Contacts of the strand formed by residues 97 - 104 (chain A) 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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.6 54.1 - - + -
95A LEU* 4.1 20.4 - - + -
96A TYR* 1.3 85.1 - - - +
98A ALA* 1.3 66.4 + - - +
118A GLN* 3.4 4.7 - - - +
119A LYS* 3.0 41.4 + - + +
121A VAL* 4.1 15.7 - - + -
129A TRP* 3.8 16.8 - - + -
131A HIS* 4.1 17.7 - - + -
133A MET* 4.9 1.6 - - - -
152A ASP 3.5 2.0 - - - -
153A GLY* 4.2 10.8 - - - +
156A HIS* 4.8 1.3 - - + -
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Residues in contact with ALA 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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81A PHE* 4.0 3.2 - - - -
96A TYR* 3.5 31.9 - - + +
97A LEU* 1.3 78.6 - - - +
99A HIS* 1.3 63.6 + - - +
100A GLU* 6.4 0.2 - - + -
117A SER 3.3 13.7 - - - +
118A GLN* 4.5 0.7 - - + -
133A MET* 3.7 4.3 - - - -
150A HIS 4.7 0.2 - - - -
151A THR* 3.4 5.1 - - - +
152A ASP* 2.8 42.4 + - + +
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Residues in contact with HIS 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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43A LEU* 4.4 5.2 - - + -
45A TRP* 4.5 2.7 - + - -
77A SER* 2.9 31.5 + - - -
78A GLN 4.6 0.2 - - - -
79A VAL* 3.5 42.8 - - + +
98A ALA* 1.3 74.9 - - - +
100A GLU* 1.3 65.7 + - - +
116A SER* 3.7 1.4 - - - -
117A SER 3.1 26.0 + - - +
133A MET* 3.2 20.3 - - + +
135A HIS* 3.8 20.0 - + - -
149A THR* 3.7 26.0 - - + +
150A HIS 3.5 4.7 + - - -
151A THR* 3.2 25.6 + - + +
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Residues in contact with GLU 100 (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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98A ALA* 6.4 0.4 - - + -
99A HIS* 1.3 79.5 - - - +
101A VAL* 1.3 68.0 + - - +
102A GLN* 3.3 33.5 + - + +
113A PRO* 3.5 26.5 - - + +
115A LEU 3.1 11.7 - - - +
116A SER* 3.9 15.8 + - - +
135A HIS* 4.8 0.7 - - - -
149A THR* 3.0 28.3 - - - -
150A HIS* 3.0 25.6 + - + +
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Residues in contact with VAL 101 (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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75A VAL* 3.6 26.9 - - + -
77A SER* 3.7 31.4 - - - +
99A HIS* 5.0 0.4 - - - +
100A GLU* 1.3 74.5 - - - +
102A GLN* 1.3 59.7 + - - +
113A PRO* 3.9 0.5 - - - +
114A LEU* 2.8 43.2 + - + +
115A LEU* 2.8 36.0 + - + -
135A HIS* 4.5 4.5 - - + +
147A LEU* 5.0 2.0 - - + -
148A SER 3.6 4.9 - - - +
149A THR* 4.0 6.7 - - + -
166A PHE* 3.7 16.6 - - + -
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Residues in contact with GLN 102 (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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100A GLU* 3.3 34.7 + - + +
101A VAL* 1.3 75.0 - - - +
103A LEU* 1.3 61.3 + - - +
104A PHE 4.1 0.2 - - - -
111A HIS* 3.3 41.4 + - + +
112A VAL 3.6 7.4 - - - +
113A PRO* 5.0 0.2 - - + -
114A LEU* 4.4 2.7 - - - -
146A GLN 3.7 0.2 - - - +
147A LEU* 3.5 9.5 - - - +
148A SER* 2.8 50.3 + - - +
150A HIS* 3.8 30.8 + - - +
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Residues in contact with LEU 103 (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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102A GLN* 1.3 75.4 - - - +
104A PHE* 1.3 73.5 + - - +
105A SER 3.4 0.2 + - - -
111A HIS* 3.5 1.8 - - - -
112A VAL* 2.9 43.4 + - + +
114A LEU* 3.9 12.8 - - + +
141A LEU* 3.9 20.2 - - + -
145A ASP* 3.8 34.1 - - + +
146A GLN 3.5 5.8 - - - +
147A LEU* 3.9 12.6 - - + -
51D ARG* 3.7 38.6 - - - +
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Residues in contact with PHE 104 (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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102A GLN 4.1 0.2 - - - -
103A LEU* 1.3 84.3 - - - +
105A SER* 1.3 80.1 + - - +
106A SER* 4.8 5.6 - - - -
110A PHE* 3.0 39.3 - + + -
111A HIS* 4.1 21.2 - + + -
145A ASP* 5.4 2.9 - - - +
146A GLN* 3.0 60.2 + - + +
148A SER* 5.6 1.7 + - - +
54H ASN* 5.8 1.9 + - - -
56H GLY* 5.7 2.9 - - - -
57H THR 4.3 15.7 - - - -
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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