Contacts of the strand formed by residues 135 - 140 (chain B) in PDB entry 1X8E
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 ALA 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B HIS 3.3 12.8 - - - +
89B PHE* 3.4 40.0 - - + +
110B LEU* 3.2 5.2 - - - +
111B GLN* 2.9 33.8 + - + +
134B TRP* 1.3 75.7 - - - +
136B HIS* 1.3 67.1 + - - +
163B ILE* 4.4 4.0 - - + -
168B PHE* 4.3 15.9 - - + -
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Residues in contact with HIS 136 (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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87B GLY* 3.2 21.7 - - - -
88B HIS* 3.0 45.5 + + - -
90B HIS* 4.6 2.2 - - - -
97B GLU* 3.6 10.1 + - + -
99B TYR* 2.5 41.2 + + - -
108B MET* 3.5 29.6 - - + -
109B LEU 3.0 13.5 - - - +
110B LEU* 3.8 5.6 - - + -
130B VAL* 3.7 10.8 - - + -
134B TRP 4.8 2.2 + - - -
135B ALA* 1.3 82.4 - - - +
137B ARG* 1.3 63.0 + - - +
138B THR 5.8 0.2 - - - -
168B PHE* 3.7 5.1 - - - -
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Residues in contact with ARG 137 (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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33B TYR* 3.3 30.1 + - - +
81B GLU* 5.0 2.6 + - - -
84B PHE* 3.2 47.9 - - + -
85B THR* 3.0 24.2 + - - +
86B LYS 3.0 20.2 + - - -
87B GLY* 4.2 1.8 - - - -
108B MET* 3.5 4.9 - - - +
109B LEU* 2.9 42.2 + - + +
136B HIS* 1.3 79.2 - - - +
138B THR* 1.3 62.3 + - - +
139B VAL* 4.1 9.2 - - + -
163B ILE* 3.5 13.3 + - - +
168B PHE* 3.7 37.7 - - + +
170B LYS 5.7 0.4 + - - -
171B ILE* 5.9 3.4 - - - +
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Residues in contact with THR 138 (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 LEU* 3.3 4.6 - - - +
84B PHE* 3.1 6.8 - - - +
85B THR* 3.0 41.5 + - - +
99B TYR* 4.3 11.4 + - + -
107B GLY 3.5 10.8 - - - +
108B MET* 4.1 14.4 - - + -
122B MET* 4.2 7.4 - - - -
136B HIS* 5.8 0.6 - - + -
137B ARG* 1.3 72.4 - - - +
139B VAL* 1.3 59.9 + - - +
146B PHE* 4.0 10.5 - - + -
148B PHE* 3.1 45.4 - - + -
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Residues in contact with VAL 139 (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 LEU* 3.9 2.2 - - - -
82B PHE* 4.0 22.4 - - + +
83B PHE 3.8 5.8 - - - +
84B PHE* 4.1 7.4 - - + -
106B GLY* 3.2 4.9 - - - -
107B GLY 2.8 31.7 + - - -
109B LEU* 4.6 3.4 - - + -
119B TRP* 3.9 22.9 - - + -
137B ARG* 4.1 22.2 - - + +
138B THR* 1.3 81.2 - - - +
140B ASN* 1.3 61.1 + - - +
141B ILE* 3.8 18.9 + - + +
146B PHE* 4.2 2.6 - - - -
172B VAL* 4.1 24.9 - - + -
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Residues in contact with ASN 140 (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 LEU* 3.2 27.5 + - + +
74B TYR 3.9 9.6 - - - +
75B PRO* 3.1 24.8 - - + +
76B GLY 4.8 1.4 + - - +
82B PHE* 3.2 27.4 - - - +
83B PHE* 3.2 14.5 + - + +
105B LYS 3.0 14.2 - - - +
139B VAL* 1.3 71.0 - - - +
141B ILE* 1.3 64.2 + - - +
142B GLY* 3.2 13.4 + - - +
144B GLU 3.0 24.7 + - - +
146B PHE* 3.5 12.6 - - + +
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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