Contacts of the strand formed by residues 129 - 133 (chain B) in PDB entry 4I93
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.8 22.7 - - + -
49B ILE* 3.7 30.1 - - + -
56B PHE* 3.9 6.5 - - + -
86B VAL* 4.2 5.4 - - + -
87B LYS 3.2 4.5 - - - +
88B ARG* 3.6 34.8 - - + -
100B PHE* 3.6 3.5 - - - -
121B CYS* 3.1 10.4 - - - +
122B CYS* 2.8 50.4 + - + +
127B GLU* 3.9 15.0 - - + +
128B ARG* 1.3 80.5 - - - +
130B LEU* 1.3 63.5 + - - +
131B ILE* 4.0 7.6 - - + -
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Residues in contact with LEU 130 (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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85B ALA 3.6 1.0 - - - +
86B VAL* 3.3 5.4 - - - +
87B LYS* 2.9 34.1 + - + -
89B PHE* 3.8 30.1 - - + -
100B PHE* 3.8 13.5 - - + -
104B ALA* 3.8 28.9 - - + -
107B VAL* 6.2 1.1 - - + -
118B LEU* 3.8 16.8 - - + -
120B GLY 3.8 0.9 - - - -
121B CYS* 4.1 2.2 - - + -
129B LEU* 1.3 74.8 - - - +
131B ILE* 1.3 62.1 + - - +
199B CYS 5.6 1.1 - - - +
200B PHE* 3.7 39.5 - - + +
203B MSE 3.9 21.3 - - + -
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Residues in contact with ILE 131 (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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44B PHE* 3.8 33.9 - - + -
49B ILE* 3.7 27.1 - - + -
84B ILE* 3.9 35.4 - - + -
85B ALA 3.4 2.9 - - - +
86B VAL* 4.4 8.3 - - + -
118B LEU* 3.3 5.5 - - - +
119B LEU* 2.7 34.8 + - + -
120B GLY 2.9 11.1 + - - +
121B CYS* 3.7 26.0 - - - -
122B CYS 4.1 0.4 - - - +
129B LEU* 4.0 14.8 - - + +
130B LEU* 1.3 77.3 - - - +
132B ALA* 1.3 55.5 + - - +
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Residues in contact with ALA 132 (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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84B ILE* 3.4 10.2 - - - +
85B ALA* 2.8 30.2 + - + +
116B ALA* 4.6 4.7 - - + +
117B ASN 3.2 14.1 - - - +
119B LEU* 4.0 6.5 - - - +
130B LEU 4.1 0.2 - - - -
131B ILE* 1.3 73.0 - - - +
133B GLU* 1.3 66.2 + - - +
199B CYS* 3.7 13.5 - - - -
200B PHE* 3.6 29.2 - - + -
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Residues in contact with GLU 133 (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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82B ARG* 4.5 12.5 + - - +
83B ARG 4.6 1.3 - - - -
85B ALA* 4.2 5.2 - - - +
111B ARG* 5.3 4.9 + - - -
115B MSE 3.6 0.2 - - - +
116B ALA* 3.8 3.5 - - - +
117B ASN* 2.8 59.8 + - - +
119B LEU* 3.9 24.1 - - + +
132B ALA* 1.3 77.5 - - - +
134B PHE* 1.3 62.6 + - - +
135B MSE 3.7 23.1 + - + +
188B LEU* 5.7 0.3 - - - +
196B ARG* 3.4 18.0 + - - -
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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