Contacts of the strand formed by residues 93 - 102 (chain B) in PDB entry 1MS4
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 ARG 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASP 3.4 24.2 + - - -
60B ASN* 3.3 26.1 + - - +
61B SER 3.3 18.2 - - - +
63B ILE* 3.4 15.5 - - + -
85B ASN* 3.5 7.5 - - - +
91B VAL* 2.8 28.4 + - - +
92B SER* 1.3 72.9 - - - +
94B VAL* 1.3 59.2 + - - +
95B VAL* 3.4 20.3 - - + +
111B GLY 3.7 0.3 - - - +
112B SER* 3.3 5.4 + - - -
113B TYR* 3.0 68.4 + - + +
116B SER* 3.1 42.8 + - - +
118B SER 3.8 6.7 + - - -
120B TRP* 5.2 2.2 - - - +
123B HIS* 4.9 0.6 + - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP* 4.4 1.4 - - - +
63B ILE* 3.3 31.8 + - - +
64B ASP* 3.9 0.4 - - - -
65B THR* 3.7 16.3 + - - +
83B ILE* 3.6 31.0 - - + +
84B LYS 4.0 15.7 - - - +
85B ASN* 4.0 7.2 - - - +
93B ARG* 1.3 75.4 - - - +
95B VAL* 1.3 65.1 + - - +
110B VAL* 3.8 22.9 - - + -
111B GLY 3.0 11.0 - - - +
112B SER* 3.9 14.6 - - - +
132B LEU* 4.4 5.2 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP* 4.4 3.6 - - - +
59B ASP 5.3 0.4 - - - +
63B ILE* 4.5 7.6 - - + -
93B ARG* 3.4 40.2 - - + +
94B VAL* 1.3 82.1 - - - +
96B ASP* 1.3 74.1 + - + +
97B PRO* 3.3 5.4 - - - -
110B VAL* 3.3 6.5 - - - +
111B GLY* 2.9 49.7 + - - +
113B TYR* 3.7 17.3 - - + -
176B LEU* 4.1 12.1 - - + -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.1 30.6 - - - +
51B ASP* 3.8 2.8 + - - -
53B ARG* 5.0 1.6 + - - -
95B VAL* 1.3 79.4 - - - +
97B PRO* 1.3 75.5 - - - +
98B THR* 3.0 13.5 + - - -
109B LEU 3.4 3.8 - - - +
110B VAL* 4.6 0.2 - - - -
119B TYR* 4.6 9.5 + - - -
176B LEU* 3.4 28.1 - - + +
177B GLY* 4.2 14.8 + - - +
179B ALA* 4.0 10.9 - - + -
195B GLN* 3.8 11.7 + - - -
230B GLU* 4.8 7.0 - - - +
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Residues in contact with PRO 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.3 12.2 - - + +
38B ALA* 4.8 2.8 - - - +
49B ILE* 4.1 12.3 - - + -
50B ALA* 4.2 12.8 - - - -
51B ASP* 3.1 21.3 - - - +
65B THR* 3.8 27.6 - - + +
94B VAL 5.3 0.2 - - - +
95B VAL* 3.4 3.8 - - - -
96B ASP* 1.3 89.8 - - - +
98B THR* 1.3 59.1 + - - +
99B VAL* 4.1 3.3 - - - +
108B VAL* 4.1 4.9 - - + -
109B LEU 3.4 8.1 - - - +
110B VAL* 3.5 14.4 - - + -
179B ALA* 3.6 0.5 - - - +
180B GLY* 3.3 21.3 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP 3.0 8.3 + - - -
97B PRO* 1.3 69.9 - - - +
99B VAL* 1.3 64.9 + - - +
108B VAL* 3.2 2.3 - - - -
109B LEU* 2.7 39.5 + - - -
177B GLY* 3.4 11.7 - - - -
178B GLY 4.2 6.1 - - - +
179B ALA 2.8 41.3 + - - +
180B GLY 3.4 4.0 - - - +
181B VAL 4.9 0.2 - - - -
182B ALA* 4.3 11.0 - - + -
192B TYR* 3.1 34.0 + - + -
193B PRO* 5.2 4.0 - - + +
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Residues in contact with VAL 99 (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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38B ALA* 4.0 18.6 - - + +
40B VAL* 4.2 19.7 - - + -
49B ILE* 3.9 31.6 - - + -
97B PRO 4.7 0.4 - - - -
98B THR* 1.3 81.5 - - - +
100B ILE* 1.3 74.7 + - - +
106B LEU* 4.2 19.1 - - + -
107B TYR 3.3 6.7 - - - +
108B VAL* 4.4 7.6 - - + -
180B GLY 2.9 15.5 + - - +
181B VAL* 3.5 6.5 - - - +
182B ALA 2.7 32.1 + - - -
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Residues in contact with ILE 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 VAL* 1.3 82.0 - - - +
101B VAL* 1.3 76.9 + - - +
105B LYS 3.7 0.7 - - - +
106B LEU* 3.6 2.9 - - - -
107B TYR* 2.7 46.3 + - + +
181B VAL* 5.2 0.9 - - - -
182B ALA* 3.7 12.8 - - + -
183B ILE* 3.7 23.6 - - - +
184B VAL* 3.9 16.4 - - + -
190B LEU* 4.0 18.4 - - + -
191B VAL 3.7 18.8 - - - +
192B TYR* 3.5 36.6 - - + +
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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
----------------------------------------------------------
40B VAL* 3.7 41.3 - - + -
41B ASN 3.7 18.8 - - - +
42B VAL* 4.0 17.5 - - + -
43B ASP 5.6 0.2 - - - +
100B ILE* 1.3 78.4 - - - +
102B LYS* 1.3 64.5 + - - +
103B GLY 4.2 13.2 - - - +
105B LYS 3.5 4.7 - - - +
106B LEU* 4.5 2.5 - - + -
181B VAL* 5.7 2.2 - - + +
182B ALA 5.3 1.2 + - - -
184B VAL* 3.0 20.6 + - - +
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Residues in contact with LYS 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 ILE 4.2 0.4 + - - -
101B VAL* 1.3 75.0 - - - +
103B GLY* 1.3 61.3 + - - +
104B ASN 3.2 0.5 + - - -
105B LYS* 3.0 32.6 + - - +
107B TYR* 4.1 17.0 - - + +
184B VAL* 3.6 21.1 - - + -
188B GLY* 2.6 34.2 + - - +
190B LEU* 3.6 15.7 - - + -
213B GLU* 2.9 38.3 + - - +
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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