Contacts of the strand formed by residues 250 - 256 (chain E) in PDB entry 6CP3
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 ASP 250 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134E LEU* 4.9 14.6 - - + +
149E ARG* 3.4 28.3 + - - +
174E ILE* 4.1 8.0 - - - +
178E HIS* 4.6 23.7 + - + +
180E GLY* 3.4 20.6 - - - -
249E GLN* 1.3 82.7 - - - +
251E VAL* 1.3 62.4 + - - +
252E LEU* 4.1 4.3 + - + +
302E GLY* 3.8 1.0 - - - -
303E SER* 2.4 34.6 + - - +
305E THR* 5.5 2.2 - - - +
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Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE 3.3 22.7 - - - +
183E VAL* 4.4 17.5 - - + -
240E ALA* 4.6 10.1 - - + -
243E PHE* 3.7 37.2 - - + -
244E ARG 4.4 2.0 - - - +
249E GLN* 4.0 23.8 - - + +
250E ASP* 1.3 78.9 - - - +
252E LEU* 1.3 67.6 + - - +
303E SER 2.9 7.3 + - - +
304E VAL* 3.2 16.4 - - + +
305E THR 2.9 24.9 + - - +
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 4.1 20.6 - - + -
136E THR* 6.3 0.7 - - + -
147E TYR* 5.8 2.7 - - + -
170E LEU* 4.5 13.2 - - + +
174E ILE* 3.7 47.1 - - + -
181E PHE 3.1 10.7 + - - +
182E SER* 3.5 8.0 - - - +
183E VAL 2.9 26.9 + - - +
250E ASP* 4.1 4.5 + - + +
251E VAL* 1.3 77.2 - - - +
253E LEU* 1.3 60.2 + - - +
254E PHE* 3.6 35.8 + - + -
305E THR* 3.2 14.8 - - + +
307E VAL* 4.7 9.0 - - + -
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E VAL* 3.4 26.7 - - + +
185E THR* 4.3 6.5 - - - +
236E GLY 3.4 23.3 - - - +
237E LEU* 4.1 25.6 - - + +
240E ALA* 4.2 5.6 - - + -
251E VAL 3.7 0.8 + - - -
252E LEU* 1.3 70.4 - - - +
254E PHE* 1.3 62.1 + - - +
255E ILE* 4.1 20.2 - - + -
296E ILE* 4.0 26.2 - - + -
304E VAL* 3.8 17.7 - - + -
305E THR 2.9 9.5 + - - +
306E SER* 3.1 10.8 + - - -
307E VAL 2.9 22.3 + - - -
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Residues in contact with PHE 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 3.5 33.0 - - + -
170E LEU* 4.0 13.2 - - + -
171E ILE* 3.5 33.9 - - + -
182E SER* 4.1 11.2 - - - -
183E VAL 2.9 9.9 + - - +
184E PHE* 3.6 28.3 - + + -
185E THR* 2.8 31.9 + - - +
252E LEU* 3.6 39.9 - - + -
253E LEU* 1.3 74.9 - - - +
255E ILE* 1.3 62.7 + - - +
256E ASP 4.2 0.2 - - - -
307E VAL* 3.2 29.8 - - + -
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Residues in contact with ILE 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E PHE* 5.5 0.4 - - - -
185E THR* 3.4 15.5 - - + +
187E VAL* 4.8 12.8 - - + -
233E ALA* 4.4 19.1 - - + +
253E LEU* 3.9 26.2 + - + -
254E PHE* 1.3 79.0 - - - +
256E ASP* 1.3 67.5 + - - +
257E ASN* 4.4 0.7 - - - +
258E ILE* 3.9 25.6 - - + +
292E LEU* 4.6 14.6 - - + -
296E ILE* 4.9 2.7 - - + -
306E SER* 4.7 4.5 - - - +
307E VAL 2.9 8.1 + - - +
308E GLN* 3.0 23.2 - - + +
309E ALA 2.9 26.3 + - - -
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Residues in contact with ASP 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E LYS* 3.7 20.0 + - - +
184E PHE* 4.5 16.7 - - + -
185E THR 3.0 5.8 + - - -
186E GLY* 3.1 7.3 - - - -
187E VAL 2.8 29.8 + - - +
189E GLU* 2.9 24.7 - - - +
254E PHE 4.2 0.2 - - - -
255E ILE* 1.3 75.9 - - - +
257E ASN* 1.3 67.5 + - - +
260E ARG* 3.4 12.4 + - - -
309E ALA* 3.3 17.9 - - + +
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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