Contacts of the strand formed by residues 237 - 241 (chain A) in PDB entry 1EQB
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 GLY 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 4.2 0.2 - - - +
95A PRO* 3.0 24.9 + - - +
97A SER* 3.3 25.4 - - - +
98A GLY 4.1 0.4 - - - -
101A ALA* 4.3 1.1 - - - -
225A THR 3.4 6.7 - - - -
227A THR* 4.8 0.7 - - - -
236A GLY* 1.3 74.3 - - - -
238A LEU* 1.3 66.6 + - - +
272A LYS* 2.9 22.2 + - - -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 4.4 19.5 - - + -
86A PHE* 4.9 7.9 - - + -
92A ASN 3.2 21.5 - - - +
93A VAL* 3.3 29.8 - - + -
95A PRO* 4.7 0.7 - - - -
101A ALA* 4.0 4.7 - - - +
224A THR* 3.2 7.4 - - - -
225A THR* 2.8 53.6 + - + +
227A THR* 4.3 18.4 - - + -
231A LEU* 5.2 1.1 - - + -
237A GLY* 1.3 74.1 - - - +
239A ILE* 1.3 66.0 + - - +
240A LEU* 4.2 16.2 - - + -
272A LYS* 5.7 1.1 - - + -
276A LEU* 4.7 10.1 - - + -
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Residues in contact with ILE 239 (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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90A TYR* 4.1 15.0 - - + +
91A ALA* 3.1 6.3 - - - -
92A ASN* 2.8 42.2 + - + +
95A PRO* 4.0 13.0 - - + -
101A ALA* 4.2 11.4 - - + +
104A ALA* 4.1 15.0 - - + -
105A VAL* 4.6 3.8 - - + -
222A VAL* 3.8 22.0 - - + -
223A VAL 3.5 8.5 - - - +
224A THR* 4.2 6.7 - - + -
238A LEU* 1.3 79.4 - - - +
240A LEU* 1.3 68.4 + - - +
252A LEU* 4.3 12.6 - - + +
256A VAL* 3.5 31.6 - - + -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 4.3 17.9 - - + +
86A PHE* 3.6 33.0 - - + -
88A ALA* 4.3 10.3 - - + -
90A TYR* 3.4 6.7 - - - +
91A ALA* 3.8 19.7 - - + -
201A MET* 3.7 22.7 - - + -
217A VAL* 4.5 6.5 - - + -
222A VAL* 3.8 2.9 - - - +
223A VAL* 2.7 43.7 + - + +
225A THR* 4.7 7.9 - - + -
238A LEU* 4.2 15.9 - - + +
239A ILE* 1.3 83.6 - - - +
241A ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 241 (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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88A ALA* 3.1 19.0 - - - +
89A ASP* 3.1 13.4 + - - +
90A TYR* 3.1 18.4 + - + -
217A VAL* 4.6 4.2 - - - +
220A ALA 5.6 0.4 - - - -
221A HIS 3.7 18.8 - - - +
222A VAL* 4.6 2.5 - - - +
223A VAL* 4.9 1.8 - - - +
240A LEU* 1.3 78.5 - - - +
242A LYS* 1.3 62.0 + - - +
244A GLY 5.6 0.2 - - - +
248A LEU* 5.6 0.2 - - + -
249A TYR* 3.6 26.5 - - + -
252A LEU* 4.8 6.7 - - + -
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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