Contacts of the strand formed by residues 95 - 100 (chain B) in PDB entry 1X2W
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 TYR 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 4.7 12.0 - - + +
115A VAL* 5.0 5.5 - - - +
116A ASN* 3.5 41.4 + - + +
70B ASN 3.0 22.2 + - - -
71B VAL* 3.3 15.0 + - + +
72B TRP* 3.2 42.3 - + + +
73B ASN* 4.3 3.6 + - - -
92B GLU* 3.8 33.8 - - + +
93B GLU 5.6 0.2 - - - -
94B SER* 1.3 79.2 - - - +
96B CYS* 1.3 58.6 + - - +
108B SER* 4.1 6.3 - - - -
109B ARG* 3.5 28.7 - - - -
110B ALA* 3.7 11.4 - - + -
111B CYS* 3.1 5.8 - - - -
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Residues in contact with CYS 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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23B TRP* 3.3 28.9 - - + -
65B TRP* 3.4 25.4 - - + -
68B LEU 3.5 4.3 - - - +
69B SER* 3.4 20.4 - - - -
71B VAL* 5.2 0.2 - - - -
95B TYR* 1.3 74.0 - - - +
97B VAL* 1.3 65.5 + - - +
98B TYR 3.9 0.2 + - - -
108B SER* 3.6 4.2 - - - -
109B ARG 2.7 33.6 + - - +
111B CYS* 2.0 43.5 - - - -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 3.8 23.3 - - + -
65B TRP* 3.7 4.8 - - - -
66B MET* 2.9 52.4 + - - +
68B LEU* 3.0 28.1 + - + -
71B VAL* 3.6 26.5 - - + -
96B CYS* 1.3 72.6 - - - +
98B TYR* 1.3 69.0 + - - +
106B TRP* 4.0 21.3 - - + -
107B ARG 3.5 11.4 - - - +
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Residues in contact with TYR 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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98A GLU* 4.9 1.9 + - - -
63B ILE* 3.5 48.6 - - + +
64B PHE 3.1 21.8 - - - +
65B TRP* 4.0 10.3 - + + -
66B MET* 3.8 10.8 - - - +
96B CYS 4.5 0.2 - - - -
97B VAL* 1.3 76.6 - - - +
99B PHE* 1.3 66.2 + - - +
100B LYS* 4.9 0.7 - - + -
106B TRP* 3.9 0.2 - - - -
107B ARG* 3.0 72.8 + - + +
108B SER 3.4 24.2 + - - -
109B ARG* 3.7 25.6 + - + -
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Residues in contact with PHE 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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40B VAL* 4.5 8.1 - - + -
42B PHE* 3.8 21.8 - + + -
51B VAL* 3.7 22.0 - - + -
52B VAL* 4.1 19.3 - - + -
55B ALA* 4.1 11.2 - - + -
64B PHE* 2.9 66.6 + + + -
65B TRP 4.6 1.6 - - - -
66B MET* 3.5 26.2 - - + -
98B TYR* 1.3 82.3 - - - +
100B LYS* 1.3 72.2 + - - +
103B ASN 4.4 5.4 - - - +
104B ASN* 5.1 3.1 - - - -
105B LYS 4.0 15.7 - - - +
107B ARG* 4.6 1.3 - - - +
118B VAL* 4.0 9.9 - - + -
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Residues in contact with LYS 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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52B VAL* 4.1 0.3 - - - +
62B SER 3.4 11.4 - - - +
63B ILE* 4.2 13.0 - - + +
98B TYR* 4.9 0.2 - - + -
99B PHE* 1.3 80.0 - - - +
101B SER* 1.3 55.3 + - - +
102B THR* 2.7 39.1 + - - +
103B ASN* 2.8 26.2 + - - +
107B ARG* 3.0 51.8 - - - +
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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