Contacts of the strand formed by residues 208 - 215 (chain B) in PDB entry 1P57
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 ARG 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET 3.1 24.2 - - - +
49A GLY* 3.9 2.2 - - - -
50A PHE* 5.9 1.2 - - + -
121B VAL* 3.9 4.5 - - - +
122B CYS* 3.3 21.9 - - - +
123B LEU 3.0 27.0 - - - +
124B PRO* 3.9 2.9 - - - +
125B ALA 4.1 3.2 + - - -
128B GLN* 3.3 20.8 - - - +
200B VAL* 3.1 5.2 - - - +
201B CYS 2.9 34.1 + - - +
203B ASP* 2.8 40.1 - - - +
205B ILE* 3.5 18.1 - - + -
206B SER* 4.0 19.6 - - - +
208B TRP* 1.3 80.8 - - + -
209B LEU* 1.3 60.0 + - - -
210B CYS* 3.3 12.9 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.8 21.3 - - - +
47B LEU* 4.6 5.2 - - + -
53B LEU* 3.4 35.9 - - + +
121B VAL* 3.8 13.3 - - + +
122B CYS 2.8 15.8 + - - +
123B LEU* 4.9 3.1 - - + -
124B PRO* 3.3 20.6 - - - +
197B GLY 5.0 0.9 - - - +
198B PRO* 3.6 31.2 - - + -
199B PHE 3.8 4.0 - - - +
200B VAL* 4.0 4.5 - - + -
208B ARG* 1.3 69.0 + - - -
210B CYS* 1.3 59.3 + - - +
211B GLY 3.3 22.7 - - - +
212B ILE* 4.6 4.5 - - + -
231B VAL* 3.4 16.3 - - + +
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 4.9 10.8 - - - -
128B GLN* 6.2 2.9 - - - -
130B LEU* 3.8 24.8 - - + +
181B PHE* 3.5 11.5 - - - -
199B PHE* 3.0 10.4 + - + +
201B CYS* 3.5 40.6 - - - -
208B ARG* 3.8 16.6 - - - -
209B LEU* 1.3 75.3 - - - +
211B GLY* 1.3 58.0 + - - +
230B LYS* 3.8 4.0 - - - +
231B VAL* 3.1 23.3 + - - -
232B SER 4.7 1.1 + - - +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B PHE* 3.7 11.4 - - - -
199B PHE* 3.1 37.7 + - - +
209B LEU* 3.3 12.5 - - - +
210B CYS* 1.3 78.9 - - - +
212B ILE* 1.3 63.9 - - - -
228B TYR* 4.3 0.4 - - - -
229B THR 3.1 12.3 - - - -
231B VAL* 3.7 2.5 - - - -
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.8 19.1 - - + +
54B THR* 3.7 16.6 - - - +
55B ALA* 4.0 5.2 - - + +
102B ASP 4.4 1.8 - - - +
103B ILE* 3.6 41.7 - - + -
196B GLY* 3.5 33.9 - - - +
197B GLY 3.3 4.3 - - - +
209B LEU* 4.6 4.3 - - + -
211B GLY* 1.3 78.4 - - - +
213B VAL* 1.3 72.5 + - - +
214B SER* 3.0 2.1 + - - -
228B TYR* 3.2 5.2 - - - -
229B THR* 3.0 37.5 + - - +
231B VAL* 3.8 13.2 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 4.1 2.6 - - - +
138B VAL* 3.7 29.8 - - + -
139B THR 5.1 1.8 - - - +
190B ALA* 3.8 11.9 - - + -
194B ASP* 3.3 29.4 - - + +
195B SER* 3.6 2.1 - - - -
196B GLY* 2.8 25.6 + - - +
197B GLY 2.9 20.5 + - - +
198B PRO 4.3 1.1 - - - +
212B ILE* 1.3 73.5 - - - +
214B SER* 1.3 58.0 + - - +
227B VAL 5.3 0.4 - - - +
228B TYR* 3.6 14.8 - - + -
346B CR4 3.5 34.1 - - + +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 5.7 0.4 - - - -
57B HIS* 3.0 26.0 + - - -
99B ASN* 4.6 1.6 + - - +
102B ASP* 2.6 32.0 + - - +
180B MET* 6.4 0.2 - - - -
195B SER* 3.7 5.0 + - - -
212B ILE 3.0 3.6 + - - -
213B VAL* 1.3 75.3 - - - +
215B TRP* 1.3 79.9 + - - +
227B VAL* 3.1 16.7 + - - -
228B TYR* 4.2 1.3 - - - -
229B THR* 3.7 21.3 + - - -
346B CR4 4.3 3.0 + - - -
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Residues in contact with TRP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN* 3.5 39.8 - - + +
174B TYR* 3.6 36.8 - + - -
175B GLN* 4.2 28.5 - - + -
176B ILE* 4.0 14.8 - - + -
180B MET* 4.1 7.4 - - - +
214B SER* 1.3 106.1 - - - +
216B GLY* 1.3 77.9 + - - +
217B THR* 4.7 3.6 - - - -
227B VAL* 2.8 55.0 + - + +
346B CR4 3.6 25.7 + - + +
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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