Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 3ITW
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 LEU 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS 3.0 13.6 + - - +
68B GLN* 3.2 26.5 - - + +
69B VAL* 2.9 25.8 + - - +
91B VAL* 3.8 24.5 - - + -
105B LEU* 4.2 29.8 - - + -
106B VAL 3.8 7.4 - - - +
107B ARG* 3.8 31.0 - - + +
111B GLY 3.6 1.6 + - - -
112B HIS* 1.3 72.4 - - - +
114B TRP* 1.3 62.5 + - - +
115B GLU* 6.4 0.4 - - + -
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Residues in contact with TRP 114 (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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5B LEU* 3.7 31.2 - - + -
7B TYR* 3.8 16.8 - - - -
17B LEU* 3.9 11.0 - - + -
21B PHE* 3.5 20.4 - + - -
23B PHE* 3.6 26.2 - + - -
42B THR* 4.5 3.8 - - + -
47B VAL* 4.5 6.7 - - + -
69B VAL* 3.5 34.8 - - + -
71B VAL* 4.0 15.9 - - + -
104B TYR 3.9 0.2 - - - +
105B LEU* 3.5 6.2 - - - +
106B VAL* 2.9 40.4 + - + +
108B ASP* 2.9 26.7 + - + +
112B HIS* 3.4 18.4 + - - +
113B LEU* 1.3 76.2 - - - +
115B GLU* 1.3 60.8 + - - +
116B PHE* 3.5 24.9 - + + -
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Residues in contact with GLU 115 (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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61A ALA* 5.8 0.3 - - - +
69B VAL 2.8 14.7 + - - +
70B ILE* 3.4 32.2 - - + +
71B VAL* 2.8 30.1 + - - +
72B TRP* 6.0 0.5 - - - -
101B LEU* 6.1 0.2 - - - +
103B GLN* 3.6 22.2 + - - +
104B TYR 3.7 4.3 - - - +
105B LEU* 3.7 24.6 - - + +
113B LEU* 6.3 0.4 - - + -
114B TRP* 1.3 72.6 - - - +
116B PHE* 1.3 64.5 + - - +
117B THR* 3.3 21.2 + - - +
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Residues in contact with PHE 116 (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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21B PHE* 3.8 24.7 - + - -
23B PHE* 4.1 8.5 - + - -
71B VAL* 3.4 34.5 - - + -
73B VAL* 3.9 13.5 - - + -
76B VAL* 3.6 10.6 - - + +
79B HIS* 3.5 39.9 - + - +
103B GLN* 3.1 22.9 - - - +
104B TYR* 3.2 39.1 + + + -
106B VAL* 3.7 16.4 - - + -
114B TRP* 3.5 30.3 - + + -
115B GLU* 1.3 72.6 - - - +
117B THR* 1.3 61.1 + - - +
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Residues in contact with THR 117 (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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70B ILE* 4.5 4.5 - - - +
71B VAL 3.0 9.9 + - - -
72B TRP* 3.3 25.7 - - + +
73B VAL* 2.9 30.3 + - - +
76B VAL* 4.6 0.4 - - - -
101B LEU* 3.9 33.9 - - + -
102B ARG 3.4 6.1 - - - +
103B GLN* 3.7 19.4 - - + +
115B GLU* 3.3 26.1 + - - +
116B PHE* 1.3 76.6 + - - +
118B ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 118 (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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72B TRP* 4.2 21.5 - - - -
73B VAL 3.3 21.3 - - - +
74B SER 4.4 12.1 - - - +
76B VAL* 3.9 13.9 - - + -
96B ASP* 5.3 3.8 + - - -
100B GLY 3.6 20.6 + - - -
101B LEU* 3.5 12.4 - - - +
102B ARG* 2.9 56.3 + - + +
117B THR* 1.3 73.4 - - - +
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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