Contacts of the strand formed by residues 141 - 145 (chain A) in PDB entry 3ISL
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 ILE 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.6 3.1 - - + -
84A VAL* 3.3 38.8 - - + +
85A ILE* 3.5 24.2 - - + -
89A ASP* 5.1 0.9 - - + -
90A ASP 3.4 2.2 + - - -
91A VAL* 3.3 23.6 - - + -
92A LEU 2.9 24.6 + - - -
139A PRO* 3.1 5.2 - - - +
140A LYS* 1.3 98.6 - - + +
142A VAL* 1.3 77.3 + - - +
143A ALA* 4.1 7.0 - - + +
170A LEU* 3.4 10.8 - - + +
172A ILE* 3.6 23.6 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.4 17.9 - - + +
94A PRO* 4.6 13.7 - - + -
130A ILE* 5.2 0.4 - - + -
134A ILE* 4.1 14.4 - - + -
139A PRO* 3.8 11.9 - - + -
141A ILE* 1.3 78.3 - - - +
143A ALA* 1.3 56.5 + - - +
144A MET* 5.1 0.4 - - + -
160A ILE* 4.4 8.5 - - + -
164A CYS* 3.3 26.9 - - - -
169A ALA* 3.8 14.4 - - + -
170A LEU 2.8 11.8 + - - +
171A PHE* 3.4 24.6 - - + -
172A ILE 2.8 31.7 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.4 16.6 - - + -
91A VAL* 4.4 3.6 - - + +
92A LEU 3.0 5.9 + - - -
93A ILE* 3.4 33.9 - - + +
94A PRO* 3.4 9.1 - - - +
103A LEU* 3.6 20.4 - - + -
141A ILE* 4.1 12.5 - - + +
142A VAL* 1.3 73.4 - - - +
144A MET* 1.3 63.4 + - - +
172A ILE* 3.2 9.4 - - + +
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PRO* 3.8 34.3 - - + +
96A TYR* 4.1 6.5 - - + -
103A LEU* 3.5 11.1 - - - +
130A ILE* 3.8 10.8 - - + -
142A VAL* 5.1 0.9 - - + -
143A ALA* 1.3 74.3 - - - +
145A VAL* 1.3 67.6 + - - +
146A HIS 3.8 0.2 + - - -
155A HIS* 3.3 54.7 - - + +
157A LEU* 4.2 11.2 - - + -
160A ILE* 3.9 17.9 - - + -
171A PHE* 4.2 20.6 - - + -
172A ILE 3.0 7.5 + - - -
173A VAL* 3.3 7.6 - - + +
174A ASP 2.8 23.9 + - - -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PRO 5.1 1.6 + - - +
96A TYR* 2.7 32.6 + - + +
99A PHE* 3.6 13.0 - - + +
100A GLY* 3.5 33.4 - - - +
103A LEU* 4.0 5.8 - - + +
144A MET* 1.3 81.2 - - - +
146A HIS* 1.3 56.1 + - - +
147A GLY 3.2 32.3 - - - +
148A GLU* 3.5 15.7 - - + +
155A HIS* 4.2 3.3 - - - +
157A LEU* 4.6 1.4 - - - +
173A VAL* 4.9 0.2 - - - -
174A ASP* 3.7 14.1 - - - +
419A PLP 3.8 17.0 - - + -
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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