Contacts of the helix formed by residues 253 - 258 (chain A) in PDB entry 2W77
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 THR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLN* 4.4 4.5 - - - +
216A ASN* 3.8 12.6 + - - -
249A LEU* 3.4 51.4 - - + +
251A GLY 4.2 2.2 + - - +
252A ALA* 1.3 82.2 - - - +
254A GLY* 1.3 63.3 + - - +
255A LEU* 3.2 3.7 + - - +
256A LEU 3.7 1.6 + - - -
257A THR* 3.2 23.3 + - - -
261A SER 4.7 1.7 + - - -
264A ALA 4.3 2.7 + - - -
265A THR* 2.7 28.7 + - - +
591A ASP 4.0 0.2 + - - -
592A ILE* 4.2 8.5 - - - +
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Residues in contact with GLY 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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252A ALA 3.5 1.0 + - - -
253A THR* 1.3 71.3 - - - +
255A LEU* 1.3 66.2 + - - +
258A GLY* 2.9 27.2 + - - -
550A ARG* 3.4 5.9 - - - -
570A ILE* 4.0 13.7 - - - +
591A ASP 2.8 25.3 + - - -
592A ILE* 3.3 19.6 - - - +
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Residues in contact with LEU 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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155A ALA 3.6 21.1 - - - +
156A THR* 3.9 10.5 - - + -
252A ALA 5.2 0.2 + - - -
253A THR* 3.2 2.9 - - - +
254A GLY* 1.3 76.4 - - - +
256A LEU* 1.3 66.9 + - + +
532A TYR* 4.1 7.3 - - + +
534A THR* 3.3 28.0 - - - +
549A GLY* 3.7 37.2 - - - +
550A ARG* 3.2 22.7 + - - +
570A ILE* 4.2 7.5 - - + +
571A PRO 5.7 0.2 - - - +
572A TYR* 3.5 42.8 - - + -
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Residues in contact with LEU 256 (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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153A ALA 4.1 2.2 - - - +
154A THR 3.5 16.8 - - - +
155A ALA 3.4 24.0 + - - +
156A THR 4.3 9.4 - - - +
157A ARG* 3.5 47.3 + - - +
218A GLN* 3.7 15.4 - - - +
223A PRO* 4.1 12.6 - - - +
253A THR 3.7 2.4 + - - -
255A LEU* 1.3 91.9 - - + +
257A THR* 1.3 66.5 + - - +
258A GLY 3.3 0.7 - - - -
532A TYR* 4.1 30.7 - - + -
534A THR* 5.7 0.4 - - - +
550A ARG* 3.6 10.9 + - - +
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Residues in contact with THR 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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216A ASN* 3.8 28.7 - - + +
218A GLN* 3.8 14.0 + - + +
223A PRO* 3.8 21.7 - - + +
253A THR* 3.2 18.8 + - - -
256A LEU* 1.3 78.1 - - - +
258A GLY* 1.3 63.5 + - - +
259A ALA 3.6 21.7 + - - +
260A GLY* 4.1 0.4 - - - -
265A THR* 2.9 27.9 + - - +
528A GLN* 3.9 5.5 - - - +
550A ARG* 4.8 3.0 + - - -
592A ILE* 4.3 0.4 - - + -
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Residues in contact with GLY 258 (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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254A GLY* 2.9 18.4 + - - -
256A LEU 3.3 2.2 - - - -
257A THR* 1.3 77.2 - - - +
259A ALA* 1.3 65.3 + - - -
528A GLN* 4.0 5.4 - - - -
550A ARG* 3.6 23.9 - - - +
552A VAL* 4.7 1.1 - - - -
570A ILE* 4.5 7.4 - - - -
592A ILE* 3.3 23.7 - - - +
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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