Contacts of the strand formed by residues 251 - 257 (chain A) in PDB entry 3ETL
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TRP* 3.5 34.1 - - + -
80A LEU* 5.1 6.7 - - + -
95A ILE* 3.5 25.1 - - + +
96A GLU 3.4 19.1 - - - +
97A SER* 3.7 14.1 - - - +
99A SER 4.1 0.7 - - - -
101A THR* 4.3 0.2 - - + -
206A LYS 3.2 2.2 + - - +
207A LEU* 3.4 19.5 - - + -
208A VAL* 3.2 21.8 + - - +
250A CYS* 1.3 76.2 - - - +
252A VAL* 1.3 70.4 + - - +
253A LEU* 3.3 36.3 - - + +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER 3.0 15.4 + - - +
100A VAL* 3.3 27.5 - - + -
101A THR 2.9 25.8 + - - -
208A VAL* 3.5 12.6 - - + +
210A ILE* 4.3 7.9 - - + -
241A LEU* 3.7 23.1 - - + +
244A LEU* 3.9 16.6 - - + -
245A ALA* 3.6 23.3 - - + -
250A CYS* 4.7 0.4 - - - -
251A ILE* 1.3 80.9 - - - +
253A LEU* 1.3 60.5 + - - +
254A VAL* 4.2 13.2 + - + -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 4.0 8.7 - - + -
101A THR* 3.4 25.1 - - + +
103A PHE* 3.5 32.3 - - + -
114A ILE* 5.2 0.2 - - + -
115A MET* 4.0 21.3 - - + -
118A THR* 3.7 39.9 - - + +
207A LEU* 4.2 4.9 - - + -
208A VAL 2.7 14.0 + - - +
209A ILE* 3.2 7.3 - - + +
210A ILE* 2.9 25.5 + - - +
251A ILE* 3.3 21.0 - - + +
252A VAL* 1.3 70.8 - - - +
254A VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.2 13.7 - - + -
101A THR 3.1 7.4 + - - +
102A GLU* 3.3 28.7 - - + -
103A PHE* 3.0 24.8 + - - +
115A MET* 4.5 2.5 - - - +
210A ILE* 3.5 28.0 - - + +
213A LEU* 3.8 30.7 - - + -
238A MET* 5.7 0.2 - - + -
241A LEU* 4.3 9.9 - - + -
252A VAL* 4.2 11.4 - - + -
253A LEU* 1.3 81.5 - - - +
255A THR* 1.3 67.3 + - - +
280A HIS* 5.2 0.7 - - - +
282A ALA* 5.5 0.4 - - + -
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Residues in contact with THR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 4.9 0.7 - - - -
103A PHE 3.3 9.0 - - - +
111A LYS* 3.8 24.5 - - + -
115A MET* 3.6 35.4 - - + -
210A ILE 3.3 4.0 + - - -
211A ASP* 2.6 30.7 + - + +
212A SER* 3.1 18.9 - - - -
213A LEU* 2.9 30.9 + - - +
214A THR 4.2 0.2 + - - -
254A VAL* 1.3 78.5 - - - +
256A ASN* 1.3 62.3 + - - +
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Residues in contact with ASN 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.3 20.2 + - - +
103A PHE 3.2 5.5 + - - -
104A ALA* 3.2 25.4 - - + +
105A GLY 3.2 7.1 + - - -
111A LYS* 3.4 7.4 - - - +
212A SER* 4.9 0.9 - - - -
213A LEU* 5.7 0.9 - - + -
214A THR* 2.5 32.8 + - - +
218A ARG* 3.7 4.6 + - - +
255A THR* 1.3 77.8 - - - +
257A GLN* 1.3 78.4 + - - +
258A VAL* 4.2 9.7 - - - +
280A HIS* 3.2 31.7 - - - +
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Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY 3.6 9.6 - - - +
106A MET 4.8 5.2 - - - -
107A PHE* 4.5 10.1 - - - +
111A LYS* 4.3 14.5 - - - +
151A GLU* 5.4 10.0 + - - +
212A SER* 5.2 7.2 + - - +
214A THR* 4.1 2.6 + - - -
215A SER* 6.1 2.6 - - - -
218A ARG* 3.1 34.4 + - - +
256A ASN* 1.3 79.4 + - - +
258A VAL* 1.3 75.8 + - - +
401A ANP 3.6 20.8 + - - +
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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