Contacts of the strand formed by residues 195 - 204 (chain C) in PDB entry 4QMG
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 VAL 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C HIS* 3.7 30.7 - - + +
193C LYS 3.6 14.1 - - - +
194C PRO* 1.3 73.2 - - - +
196C ASN* 1.3 79.0 + - - +
197C ALA* 3.4 2.5 + - + +
212C LEU* 4.1 22.4 - - + -
213C LEU 3.7 15.3 - - - +
262C GLN* 3.2 4.0 - - - -
263C ILE* 2.8 43.6 + - + +
265C LEU* 4.1 18.4 - - + -
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Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C PRO 4.1 1.6 + - - +
195C VAL* 1.3 77.7 - - - +
197C ALA* 1.3 60.9 + - - +
213C LEU* 2.9 49.2 + - + +
261C VAL 3.7 4.4 - - - +
262C GLN* 3.2 29.8 + - - +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C VAL 4.0 5.8 - - - +
196C ASN* 1.3 76.7 - - - +
198C ILE* 1.3 64.5 + - - +
210C ALA* 4.7 1.6 - - + -
211C LEU 3.2 13.7 - - - +
212C LEU* 4.1 11.9 - - + -
213C LEU* 4.6 3.7 - - - +
259C ARG 3.8 0.2 - - - +
260C ASP* 3.8 2.9 - - - -
261C VAL* 2.9 36.9 + - + +
263C ILE* 3.7 32.3 - - + -
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Residues in contact with ILE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PHE* 4.5 2.9 - - + -
83C ARG* 4.2 4.3 - - - +
84C GLU* 3.4 20.2 - - - +
87C ARG* 3.4 53.6 - - - +
197C ALA* 1.3 78.8 - - - +
199C ILE* 1.3 65.3 + - - +
200C GLU* 3.2 19.0 + - - +
210C ALA* 3.3 1.7 - - - -
211C LEU* 2.8 54.1 + - + +
213C LEU* 4.7 17.7 - - + -
258C GLN* 4.2 7.4 - - - -
259C ARG 3.7 4.0 - - - +
260C ASP* 4.2 3.4 - - - +
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ILE* 1.3 72.4 - - - +
200C GLU* 1.3 60.1 + - - +
201C HIS 3.8 18.6 - - - +
202C VAL* 4.2 10.1 - - + -
208C VAL* 4.1 21.5 - - + -
209C ARG 3.7 3.1 - - - +
210C ALA* 4.2 12.8 - - + -
256C LEU* 3.2 35.2 - - + +
257C LEU* 3.8 1.1 - - - -
258C GLN* 2.6 32.4 + - - -
259C ARG 3.5 4.2 + - - -
261C VAL* 3.7 33.0 - - + -
263C ILE* 4.2 3.1 - - + -
277C ILE* 4.1 22.7 - - + -
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C MSE 5.3 2.4 - - - +
80C PHE* 4.8 0.5 - - - -
83C ARG* 2.9 43.5 + - - -
174C ARG* 4.9 5.1 + - - -
198C ILE* 3.2 18.2 + - - +
199C ILE* 1.3 73.9 - - - +
201C HIS* 1.3 86.8 + - + +
209C ARG 2.7 13.8 + - - +
211C LEU* 3.7 31.9 - - + +
218C LEU* 4.2 14.8 - - + -
257C LEU* 3.5 11.1 - - - +
258C GLN* 4.4 10.5 + - - +
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Residues in contact with HIS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C MSE 5.3 12.5 - - - -
28C LEU* 6.5 0.7 - - + -
61C ARG* 5.4 9.5 + - - -
199C ILE* 3.6 1.8 - - - +
200C GLU* 1.3 102.5 + - + +
202C VAL* 1.3 67.5 + - - +
203C ARG* 5.2 1.8 - - + +
208C VAL* 3.4 7.8 - - - +
209C ARG* 2.8 51.9 + - + +
218C LEU* 5.7 5.6 - - + -
257C LEU* 4.0 4.9 - - - +
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ILE* 4.2 10.1 - - + -
201C HIS* 1.3 80.4 - - - +
203C ARG* 1.3 62.5 + - - +
204C ASP 3.2 28.5 - - - +
207C VAL 4.0 2.9 - - - +
208C VAL* 3.9 14.6 - - + -
249C LYS* 3.2 42.4 + - + +
252C THR* 4.5 9.6 - - + +
253C GLU* 4.1 35.2 + - + +
256C LEU 5.6 0.2 - - - -
257C LEU* 4.4 8.5 - - + +
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Residues in contact with ARG 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C HIS* 4.1 2.2 + - + -
202C VAL* 1.3 73.8 - - - +
204C ASP* 1.3 63.9 + - - +
207C VAL* 3.0 30.4 + - + +
209C ARG* 3.6 45.7 - - + +
220C THR* 3.9 20.1 + - - +
231C PHE* 3.7 18.2 - - - -
249C LYS* 4.0 6.8 + - - +
272C ASN* 5.2 2.2 + - - +
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Residues in contact with ASP 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 3.2 15.3 - - - +
203C ARG* 1.3 77.6 - - - +
205C GLY* 1.3 66.4 + - - +
206C SER* 3.0 10.0 + - - -
207C VAL* 2.8 54.8 + - - +
208C VAL* 4.6 0.7 - - - +
228C CYS* 3.7 6.1 - - - +
229C PRO 3.5 13.8 - - - +
230C THR* 3.2 28.8 - - - +
231C PHE* 4.2 14.8 - - + +
245C ALA 5.4 0.2 - - - +
249C LYS* 4.2 11.9 - - + -
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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