Contacts of the strand formed by residues 194 - 206 (chain A) in PDB entry 6H60
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 GLN 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.2 19.1 - - - +
182A LYS 3.3 19.3 + - - +
183A LEU 5.2 1.0 + - - -
192A LYS 3.7 3.2 + - - -
193A LEU* 1.3 72.5 - - - +
195A GLN* 1.3 65.0 + - - +
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Residues in contact with GLN 195 (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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179A PRO* 4.0 13.9 - - - -
180A VAL 3.3 12.6 - - - -
181A LEU* 3.9 2.0 - - - +
193A LEU 4.2 1.4 + - - -
194A GLN* 1.3 74.1 - - - +
196A ARG* 1.3 58.0 + - - +
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Residues in contact with ARG 196 (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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178A ARG 2.5 23.3 - - - +
179A PRO* 3.6 2.7 - - - -
180A VAL* 2.4 31.7 + - - +
194A GLN 3.8 0.6 + - - -
195A GLN* 1.3 73.5 - - - +
197A GLN* 1.3 60.1 + - - +
198A LEU* 3.3 0.9 + - - -
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Residues in contact with GLN 197 (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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40A ASP* 4.8 2.6 - - - -
41A LEU 4.7 10.0 + - - -
42A GLY* 4.8 6.4 + - - -
177A PHE* 4.6 5.8 - - - +
178A ARG 3.1 13.0 - - - +
179A PRO* 4.2 1.7 - - - +
196A ARG* 1.3 70.9 - - - +
198A LEU* 1.3 58.2 + - - +
199A ILE 4.2 0.4 + - - -
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Residues in contact with LEU 198 (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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38A ASP* 5.2 2.8 - - - -
39A CYS 3.2 15.3 - - - +
40A ASP* 4.9 0.9 - - - +
176A ARG 3.5 1.6 - - - +
177A PHE* 3.5 4.6 - - - -
178A ARG* 2.9 31.4 + - - +
180A VAL* 5.6 0.7 - - - +
196A ARG 3.3 1.3 + - - -
197A GLN* 1.3 72.3 - - - +
199A ILE* 1.3 68.1 + - - +
200A THR* 4.7 0.2 - - - -
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Residues in contact with ILE 199 (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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38A ASP* 3.1 5.2 - - - -
39A CYS 2.9 33.8 + - - -
41A LEU* 5.1 3.4 - - - +
175A GLY 5.1 1.6 - - - -
176A ARG 3.4 10.1 - - - -
177A PHE* 4.4 1.7 - - - +
197A GLN 4.2 0.4 - - - -
198A LEU* 1.3 72.6 - - - +
200A THR* 1.3 60.0 + - - +
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Residues in contact with THR 200 (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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37A ALA 3.6 6.3 - - - -
38A ASP* 4.4 2.2 - - - +
158A ASP 6.0 1.1 - - - -
174A VAL* 3.0 5.5 - - - -
175A GLY* 2.8 33.7 + - - +
176A ARG 3.3 11.2 + - - -
198A LEU 3.8 0.4 + - - -
199A ILE* 1.3 73.7 - - - +
201A VAL* 1.3 58.1 + - - +
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Residues in contact with VAL 201 (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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36A THR* 3.6 1.7 - - - -
37A ALA* 2.9 36.5 + - - +
173A ALA 3.4 4.0 - - - -
174A VAL* 4.1 2.5 - - - +
199A ILE 4.3 0.2 + - - -
200A THR* 1.3 73.3 - - - +
202A THR* 1.3 60.9 + - - +
203A MET 3.9 1.0 + - - -
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Residues in contact with THR 202 (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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35A ALA 3.2 11.9 - - - -
36A THR* 4.3 2.2 - - - +
160A PHE 5.5 6.7 - - - -
171A ILE 3.6 0.9 - - - +
172A LEU* 3.4 4.3 - - - -
173A ALA* 2.3 53.5 + - - +
201A VAL* 1.3 67.3 - - - +
203A MET* 1.3 62.0 + - - +
204A SER 3.8 0.3 + - - -
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Residues in contact with MET 203 (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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33A ALA 3.7 0.5 - - - +
34A TYR* 3.1 2.8 - - - -
35A ALA* 2.5 43.2 + - - +
171A ILE 3.8 3.6 - - - -
172A LEU* 4.9 1.8 - - - +
201A VAL 3.9 2.4 + - - -
202A THR* 1.3 70.8 - - - +
204A SER* 1.3 62.4 + - - +
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Residues in contact with SER 204 (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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33A ALA 3.3 5.6 - - - -
34A TYR* 4.3 2.7 - - - +
170A CYS* 3.2 24.4 - - - -
171A ILE 2.9 19.3 + - - +
202A THR 3.8 0.8 + - - -
203A MET* 1.3 73.3 - - - +
205A SER* 1.3 58.1 + - - +
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Residues in contact with SER 205 (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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32A HIS* 4.3 1.8 - - - -
33A ALA* 2.2 62.9 + - - +
169A ALA 3.5 9.9 - - - -
170A CYS* 4.7 0.2 - - - +
203A MET 4.0 0.4 + - - -
204A SER 1.3 70.4 - - - -
206A ASP* 1.3 57.6 + - - +
210A VAL* 5.8 2.2 - - - +
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Residues in contact with ASP 206 (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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30A VAL* 5.7 2.0 - - - +
31A PRO 3.6 10.3 - - - -
32A HIS* 4.3 4.5 - - - +
169A ALA* 3.4 14.6 + - - +
205A SER* 1.3 71.1 - - - +
207A SER* 1.3 61.3 + - - +
208A ARG 3.2 2.5 - - - +
209A VAL* 3.5 3.1 + - - +
210A VAL* 2.7 36.9 + - - +
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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