Contacts of the strand formed by residues 71 - 83 (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 GLY 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B THR 3.8 0.8 + - - -
70B SER* 1.3 74.1 - - - +
72B ILE* 1.3 64.0 + - - -
73B TYR* 3.2 14.1 - - - -
140B GLN* 4.6 1.8 - - - -
141B LEU 3.0 29.5 + - - +
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Residues in contact with ILE 72 (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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30A ALA* 4.7 2.5 - - + -
53A PHE* 3.5 31.2 - - + -
55A GLN* 3.4 38.6 - - - +
71B GLY* 1.3 75.1 - - - -
73B TYR* 1.3 69.3 + - - +
138B ALA* 4.1 15.5 - - + -
139B PHE 3.6 8.7 - - - +
140B GLN* 4.0 19.3 - - + +
170B ALA* 3.6 2.4 - - - +
171B LEU* 3.0 53.7 + - + +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 4.6 1.8 - - + +
58B PHE* 3.8 29.6 - + - -
67B VAL* 3.4 15.5 - - + +
68B PRO* 3.7 5.0 - - + +
69B THR* 2.4 47.5 + - - -
70B SER 4.8 0.2 - - - -
71B GLY* 3.2 33.0 - - - -
72B ILE* 1.3 77.0 - - - +
74B PHE* 1.3 62.0 + - - +
75B VAL* 3.5 11.3 + - + +
138B ALA* 3.3 3.2 - - - -
139B PHE* 2.9 30.5 + - - +
141B LEU* 4.0 27.8 - - + -
147B LEU* 6.5 0.2 - - + -
168B ALA* 5.1 1.1 - - + -
169B PHE* 3.4 8.7 - - - +
170B ALA* 3.6 35.7 - - + +
171B LEU* 4.5 0.4 - - - -
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Residues in contact with PHE 74 (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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74A PHE* 4.1 19.7 - + - -
76A TYR* 4.7 3.6 - + - -
134A TYR* 3.7 17.7 - + - -
169A PHE* 3.9 18.6 - + + -
73B TYR* 1.3 71.3 - - - +
75B VAL* 1.3 57.4 + - - +
76B TYR* 4.0 17.3 - + + -
134B TYR* 4.9 2.2 - - - -
136B GLY* 3.5 12.8 - - - -
137B ALA* 3.3 33.0 - - - -
138B ALA* 4.0 2.0 - - - +
168B ALA* 3.2 4.3 - - - -
169B PHE* 2.9 73.5 + + + -
171B LEU* 4.0 11.1 - - + +
74D PHE* 3.7 26.2 - + - -
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Residues in contact with VAL 75 (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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73B TYR* 3.9 17.0 - - + +
74B PHE* 1.3 79.5 - - - +
76B TYR* 1.3 64.8 + - - +
101B VAL* 3.9 27.6 - - + -
114B LEU* 5.5 0.4 - - + -
115B LEU* 3.6 5.4 - - + +
136B GLY* 2.9 21.5 - - - -
137B ALA 2.8 15.0 + - - -
139B PHE* 3.9 21.8 - - + -
141B LEU* 4.4 3.1 - - + -
147B LEU* 3.8 30.3 - - + -
166B PHE* 4.2 7.4 - - + -
167B GLY 3.6 9.0 - - - +
168B ALA* 4.1 6.7 - - + -
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Residues in contact with TYR 76 (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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31B ALA 4.1 0.7 + - - -
32B HIS* 2.7 30.1 + - - +
74B PHE* 4.0 21.8 - + + -
75B VAL* 1.3 78.0 - - - +
77B SER* 1.3 65.4 + - - +
101B VAL* 5.0 0.9 - - - -
115B LEU* 4.6 1.1 - - - -
134B TYR* 3.8 14.4 - - - +
135B HIS 3.3 12.3 - - - +
136B GLY* 3.9 4.5 - - - -
165B PHE* 3.8 15.5 - + - -
166B PHE* 3.5 3.9 - - - -
167B GLY* 2.8 61.3 + - - +
168B ALA* 3.7 3.8 - - - -
169B PHE* 4.3 15.0 - + - -
74D PHE* 4.4 1.6 - + - -
136D GLY 3.8 11.0 - - - -
137D ALA* 3.5 18.4 - - + -
138D ALA* 3.0 27.4 + - + +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.6 1.0 - - - -
76B TYR* 1.3 80.7 - - - +
78B GLN* 1.3 58.5 + - - +
99B HIS* 2.9 28.2 + - - -
101B VAL* 3.6 25.3 - - - +
133B MET 3.9 0.9 - - - +
134B TYR* 3.6 4.6 - - - -
135B HIS* 3.0 36.5 + - - +
149B THR* 4.3 0.3 - - - +
165B PHE* 3.0 19.3 + - - -
166B PHE* 4.0 9.7 - - - +
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Residues in contact with GLN 78 (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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77B SER* 1.3 73.8 + - - +
79B VAL* 1.3 78.4 + - - +
80B VAL* 4.4 2.0 - - - +
99B HIS* 4.7 0.4 - - - -
132B SER* 4.6 9.2 + - - +
133B MET 3.2 11.4 - - - +
134B TYR* 3.7 11.6 - - + +
162B SER 3.3 21.4 + - - -
163B THR* 3.1 22.2 + - - +
164B VAL* 3.3 1.9 - - - +
165B PHE* 2.9 59.3 + - + +
116D SER 4.1 6.6 + - - -
117D SER* 4.3 1.4 + - - -
134D TYR 4.1 2.8 - - - +
135D HIS* 3.1 35.8 - - - +
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Residues in contact with VAL 79 (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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43B LEU* 4.9 3.4 - - + -
78B GLN* 1.3 79.7 - - - +
80B VAL* 1.3 68.6 + - - +
81B PHE* 3.7 22.9 - - + -
99B HIS* 3.4 50.9 - - + +
132B SER* 3.5 1.2 + - - -
133B MET* 2.8 46.4 + - + +
151B THR* 5.1 0.4 - - - +
157B LEU* 3.8 21.5 - - + -
163B THR 3.7 3.8 - - - -
164B VAL* 3.8 11.2 - - + -
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Residues in contact with VAL 80 (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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78B GLN* 4.4 5.4 - - - +
79B VAL* 1.3 78.9 - - - +
81B PHE* 1.3 61.5 + - - +
130B LEU* 3.7 28.5 - - + -
131B HIS 3.5 7.4 - - - +
132B SER* 3.7 15.9 - - - +
157B LEU* 3.4 5.6 - - - +
158B VAL* 2.8 50.3 + - + -
163B THR* 3.3 37.3 + - + +
164B VAL* 3.8 3.0 - - + +
116D SER 5.3 3.1 - - - +
117D SER* 5.4 2.0 - - - +
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Residues in contact with PHE 81 (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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79B VAL* 3.7 26.9 - - + -
80B VAL* 1.3 73.5 - - - +
82B SER* 1.3 61.5 + - - +
97B LEU* 3.9 23.6 - - + -
98B ALA 3.7 21.3 - - - -
129B TRP* 3.7 18.6 - - + -
130B LEU* 3.3 7.9 - - - +
131B HIS* 2.8 39.4 + - + +
133B MET* 3.8 20.4 - - + -
151B THR* 3.9 8.7 - - + -
152B ASP 3.6 12.3 - - - -
153B GLY 3.3 29.4 - - - -
156B HIS* 3.2 12.8 - - + +
157B LEU* 3.7 19.1 - - + -
158B VAL* 4.3 0.7 - - - -
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Residues in contact with SER 82 (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* 1.3 75.4 - - - +
83B GLY* 1.3 58.5 + - - +
129B TRP* 3.2 25.4 - - - -
130B LEU* 3.6 15.7 - - - -
156B HIS* 3.1 32.1 + - - +
158B VAL* 3.5 16.3 - - - +
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Residues in contact with GLY 83 (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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82B SER* 1.3 79.0 - - - +
84B LYS* 1.3 68.1 + - - -
128B PRO* 3.3 8.2 - - - +
129B TRP* 3.2 34.2 + - - -
156B HIS* 4.5 4.9 - - - -
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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