Contacts of the strand formed by residues 185 - 193 (chain H) in PDB entry 6BCH
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 185 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181H THR* 2.8 25.8 + - - +
182H ALA 5.6 0.2 - - - +
183H GLY 3.6 2.1 - - - +
184H GLU* 1.3 82.6 - - - +
186H SER* 1.3 61.2 + - - -
187H PHE* 5.2 4.5 - - - -
207H PHE* 4.8 3.1 - - - -
208H GLN 3.3 9.6 - - - -
209H ILE* 4.2 9.2 - - - -
274H LYS* 6.0 1.6 - - - +
16J G 4.3 5.2 - - - +
17J A 3.7 6.6 + - - -
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Residues in contact with SER 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H GLU 5.1 0.4 - - - -
185H GLY* 1.3 73.1 - - - -
187H PHE* 1.3 65.9 + - - +
188H TYR* 3.3 24.6 + - - +
206H VAL 3.7 1.0 - - - +
207H PHE* 3.4 7.8 - - - -
208H GLN* 2.9 46.4 + - - +
310H ASN* 4.8 0.7 + - - -
16J G 4.0 14.2 - - - +
17J A 2.3 32.6 + - - -
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Residues in contact with PHE 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H THR* 5.3 2.9 - - - -
185H GLY 5.2 3.1 - - - -
186H SER* 1.3 77.6 + - - +
188H TYR* 1.3 60.0 + - - +
206H VAL 3.6 3.6 - - - -
207H PHE* 3.3 37.7 - + - -
261H ILE* 4.5 0.2 - - + -
265H PHE* 4.0 16.2 - + - -
270H ILE* 4.2 22.7 - - + -
274H LYS* 4.9 7.9 - - + -
277H ASP* 5.1 3.0 - - + +
278H TYR* 3.4 45.1 - + + +
281H TRP* 3.4 51.8 - + + -
309H MET* 3.7 8.3 - - - +
310H ASN* 3.5 19.0 + - - +
17J A 4.5 0.8 + - - -
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Residues in contact with TYR 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H SER* 3.3 22.0 - - - -
187H PHE* 1.3 74.9 - - - +
189H ILE* 1.3 73.0 + - - +
190H ARG* 4.0 19.8 + - + -
206H VAL* 2.9 72.6 + - + +
208H GLN* 3.0 38.8 + - + -
250H VAL* 5.3 2.1 - - - +
281H TRP* 3.3 3.8 + - - +
309H MET* 4.8 2.0 - - - -
310H ASN* 3.8 5.6 - - - +
17J A 4.2 10.1 - + + -
18J C 3.7 56.2 + + - +
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Residues in contact with ILE 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H TYR* 1.3 79.1 - - - +
190H ARG* 1.3 63.5 + - - +
191H ILE* 3.8 10.9 + - + +
203H VAL* 4.1 13.9 - - + -
204H GLN 3.5 5.8 - - - +
205H SER* 3.8 20.6 - - - -
281H TRP* 3.6 25.1 - - + +
284H VAL* 3.7 35.7 - - + -
288H ILE* 5.0 0.2 - - + -
302H ILE* 3.9 25.6 - - + -
306H LYS* 4.7 17.3 - - + +
309H MET* 4.5 12.8 - - - +
18J C 5.5 1.4 + - - -
19J G 5.4 2.4 + - - -
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Residues in contact with ARG 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H TYR* 3.9 27.6 + - + -
189H ILE* 1.3 72.1 - - - +
191H ILE* 1.3 63.2 + - - +
192H ALA* 4.9 2.2 - - + +
202H GLN 3.6 1.0 - - - +
203H VAL* 3.5 4.2 - - - -
204H GLN* 2.9 63.2 + - + +
206H VAL* 4.1 16.1 - - + +
250H VAL* 5.3 4.0 - - - +
252H THR* 4.0 18.6 - - - +
7I A 3.8 9.7 + - - -
8I A 3.5 22.2 + - - +
9I C 3.8 7.9 - - - +
18J C 4.9 2.2 - - - +
19J G 3.3 35.7 + - + +
20J T 3.4 29.6 + - + +
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Residues in contact with ILE 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H ILE* 3.8 19.0 + - + +
190H ARG* 1.3 79.0 - - - +
192H ALA* 1.3 61.5 + - - +
193H LYS 4.2 0.6 + - - +
201H TYR* 4.6 22.0 - - + -
202H GLN 3.4 4.7 - - - +
203H VAL* 4.4 15.9 - - + -
299H LEU* 4.9 7.4 - - + -
302H ILE* 4.6 9.2 - - + -
303H GLN* 4.1 23.8 - - - +
306H LYS* 5.9 2.9 - - + -
19J G 4.1 28.9 + - - +
20J T 4.2 12.2 + - - +
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Residues in contact with ALA 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H ARG* 4.2 2.7 - - + -
191H ILE* 1.3 75.2 - - - +
193H LYS* 1.3 64.5 + - - +
194H ASN* 3.8 1.2 - - + +
201H TYR* 3.1 6.8 - - - -
202H GLN* 2.9 44.0 + - + +
7I A 5.8 0.9 - - - +
20J T 3.6 29.8 - - + -
21J T 4.2 22.7 - - + +
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Residues in contact with LYS 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H ILE* 4.2 0.8 + - - +
192H ALA* 1.3 69.8 - - - +
194H ASN* 1.3 60.0 + - - +
200H GLY 3.7 1.6 - - - +
201H TYR* 3.5 28.3 - - + +
20J T 3.7 23.4 + - - +
21J T 3.9 18.2 + - - +
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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