Contacts of the strand formed by residues 92 - 99 (chain M) in PDB entry 2A3W
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 VAL 92 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M ARG* 3.3 7.6 - - - +
39M ALA* 2.8 51.7 + - + +
65M LYS* 6.1 1.1 - - - +
71M TYR* 3.6 21.5 - - - +
86M GLU* 4.3 4.5 - - - +
90M ALA 4.2 6.3 - - - +
91M PRO* 1.3 76.4 - - - +
93M HIS* 1.3 65.3 + - - +
94M ILE* 3.6 25.4 + - + +
109M ILE* 3.7 24.7 - - + -
110M ASN* 3.7 10.5 - - - +
203M TRP* 4.8 0.8 - - - -
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Residues in contact with HIS 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M CYS* 4.2 5.9 - - - +
37M PHE* 3.6 15.4 + - - -
38M ARG* 3.7 36.8 - - + +
92M VAL* 1.3 74.2 - - - +
94M ILE* 1.3 62.8 + - - +
95M CYS* 3.3 33.1 + - - -
108M TRP 3.6 1.5 + - - +
109M ILE* 3.5 4.7 - - - -
110M ASN* 2.8 37.4 + - - +
111M GLY 4.9 3.6 + - - -
156M ASP* 5.3 4.1 + - + +
169M ILE* 4.4 1.3 - - + +
172M ALA* 3.5 15.7 + - - +
173M TYR* 3.5 50.0 - + + +
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Residues in contact with ILE 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M LEU 3.8 0.5 - - - +
36M CYS* 3.2 3.1 - - - -
37M PHE* 2.8 73.4 + - + +
39M ALA* 4.5 2.9 - - + -
49M LEU* 3.8 11.9 - - + -
63M VAL* 4.9 2.5 - - + -
71M TYR* 3.6 22.2 - - + -
92M VAL* 3.6 24.5 - - + +
93M HIS* 1.3 78.8 - - - +
95M CYS* 1.3 74.3 + - - +
96M VAL* 4.8 1.3 - - + +
107M PHE* 4.3 15.0 - - + -
108M TRP 3.5 2.7 - - - -
109M ILE* 3.8 25.1 - - + -
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Residues in contact with CYS 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M THR* 4.9 1.3 - - + -
35M LEU 3.1 4.3 - - - -
36M CYS* 2.0 46.9 - - - -
93M HIS* 3.3 25.1 + - - -
94M ILE* 1.3 75.0 - - - +
96M VAL* 1.3 59.9 + - - +
106M GLU 4.2 0.4 - - - -
107M PHE* 3.4 6.6 - - - -
108M TRP* 2.8 38.8 + - + +
169M ILE* 3.8 35.0 - - + -
172M ALA* 4.5 1.6 - - - -
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Residues in contact with VAL 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M PHE* 4.0 10.2 - - + -
34M THR* 3.4 3.2 - - - -
35M LEU* 2.8 54.2 + - + +
37M PHE* 5.6 0.7 - - + -
63M VAL* 3.8 28.9 - - + -
73M LEU* 3.9 24.5 - - + -
94M ILE* 5.4 2.0 - - + -
95M CYS* 1.3 76.4 - - - +
97M SER* 1.3 65.0 + - - +
106M GLU 3.1 12.6 - - - +
107M PHE* 3.7 33.4 - - + -
108M TRP* 5.6 0.2 - - - -
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Residues in contact with SER 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M PHE* 3.1 14.8 - - - -
34M THR* 3.4 19.5 - - - -
96M VAL* 1.3 79.4 - - - +
98M TRP* 1.3 61.8 + - - +
104M ILE 4.4 0.9 + - - -
105M ALA* 3.2 5.0 - - - +
106M GLU* 2.8 52.5 + - - +
108M TRP* 5.7 1.1 - - - -
163M VAL* 3.7 23.4 - - - +
164M LEU 4.8 1.8 - - - -
169M ILE* 5.8 2.0 - - - -
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Residues in contact with TRP 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LEU 4.2 4.7 - - - -
31M GLN 3.4 24.0 - - - -
32M ASN* 3.4 4.9 - - - -
33M PHE* 3.0 65.5 + + + +
73M LEU* 4.2 5.6 - - + -
75M ILE* 3.8 25.8 - - + -
97M SER* 1.3 76.2 - - - +
99M GLU* 1.3 65.6 + - - +
100M SER* 3.8 11.0 - - - -
103M GLY 3.2 19.5 + - - -
104M ILE 3.3 7.9 - - - -
105M ALA* 4.2 2.0 - - + -
119M LEU* 3.0 35.9 + - + +
120M ARG 3.2 22.4 - - - -
123M TYR 3.1 28.9 - - - -
125M VAL* 3.6 20.2 - - + -
163M VAL* 3.7 5.2 - - - +
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Residues in contact with GLU 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L LYS* 2.7 29.2 + - - -
32M ASN* 3.6 17.5 - - - +
98M TRP* 1.3 77.5 - - - +
100M SER* 1.3 54.9 + - - +
101M SER* 3.7 19.0 + - - +
102M SER* 2.7 25.3 + - - +
103M GLY* 2.6 37.8 + - - -
104M ILE* 3.1 12.0 + - + +
163M VAL* 3.9 24.2 - - + +
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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