Contacts of the strand formed by residues 192 - 206 (chain A) in PDB entry 3C0M
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 SER 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.6 22.9 - - - +
190A THR 4.1 1.6 + - - -
191A GLN* 1.3 79.0 - - - +
193A ASP* 1.3 71.4 + - - +
251A GLY* 5.8 2.9 - - - -
252A GLU 5.9 0.2 + - - -
253A THR* 4.8 5.2 - - - +
301A ASP 3.4 7.9 - - - -
302A ILE* 4.3 8.7 - - - +
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Residues in contact with ASP 193 (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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191A GLN* 3.8 14.2 + - - +
192A SER* 1.3 84.6 + - - +
194A ARG* 1.3 63.7 + - - +
195A GLN* 6.0 0.9 - - - +
253A THR* 4.9 3.5 - - - +
299A LYS* 4.8 10.2 + - - +
300A ALA* 3.3 5.5 - - - +
301A ASP* 2.7 53.5 + - - +
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Residues in contact with ARG 194 (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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193A ASP* 1.3 77.9 - - - +
195A GLN* 1.3 68.0 + - - +
252A GLU* 4.1 46.8 + - + +
253A THR* 5.0 6.1 - - + +
298A TYR* 3.4 48.9 + - + -
299A LYS 3.9 1.1 - - - +
300A ALA* 3.8 19.5 - - + -
410A PHE* 4.8 12.2 - - - -
110B ALA* 4.6 21.4 - - - +
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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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193A ASP* 5.5 1.1 + - - +
194A ARG* 1.3 76.4 - - - +
196A LEU* 1.3 67.4 + - - +
197A VAL* 3.4 25.5 + - - +
298A TYR* 3.6 10.5 - - - -
299A LYS* 3.0 65.9 + - + +
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Residues in contact with LEU 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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195A GLN* 1.3 77.3 + - - +
197A VAL* 1.3 59.9 + - - +
198A LYS* 3.7 25.6 - - - +
199A THR* 3.8 18.2 - - - +
296A GLU* 3.9 25.1 - - + +
297A LEU 3.7 8.5 - - - +
298A TYR* 4.0 15.7 - - + -
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Residues in contact with VAL 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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195A GLN* 3.4 26.9 + - - +
196A LEU* 1.3 72.6 - - - +
198A LYS* 1.3 66.2 + - + +
297A LEU* 3.1 26.4 + - + +
299A LYS* 3.5 35.2 - - + +
409A GLN* 5.8 1.6 - - - +
455A LEU* 3.9 29.9 - - + +
457A PHE* 4.1 13.9 - - + -
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Residues in contact with LYS 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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196A LEU* 3.2 9.1 - - - +
197A VAL* 1.3 91.9 - - + +
199A THR* 1.3 73.7 + - - +
200A VAL* 4.4 11.9 - - + +
296A GLU* 3.6 1.0 - - - -
297A LEU* 2.7 43.2 + - + +
451A GLU* 4.1 26.3 + - - +
452A LEU* 3.5 32.8 - - + -
455A LEU* 4.2 12.8 - - + -
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Residues in contact with THR 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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196A LEU* 3.8 14.6 - - - +
198A LYS* 1.3 85.7 + - - +
200A VAL* 1.3 63.0 + - - +
201A VAL* 3.5 21.0 + - + +
294A LYS* 3.4 36.6 - - + -
295A ILE 3.5 4.7 - - - +
296A GLU* 3.8 14.9 - - + +
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Residues in contact with VAL 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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198A LYS* 4.4 14.8 - - - +
199A THR* 1.3 73.0 - - - +
201A VAL* 1.3 62.1 + - - +
293A VAL* 3.6 1.7 - - - +
294A LYS* 3.5 3.5 - - - -
295A ILE* 2.7 57.8 + - + +
297A LEU* 4.3 22.0 - - + -
445A ILE* 4.4 18.2 - - + -
446A PRO 4.6 7.6 - - - +
447A LEU* 3.9 29.4 - - + -
452A LEU* 4.6 4.7 - - + -
462A LEU* 4.9 3.6 - - + -
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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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199A THR* 3.5 33.4 + - + +
200A VAL* 1.3 77.0 - - - +
202A GLY* 1.3 60.3 + - - +
293A VAL 3.4 4.7 - - - +
294A LYS* 3.8 15.9 - - + -
445A ILE* 3.4 17.6 - - - +
446A PRO* 3.9 11.1 - - - +
135B TYR* 5.0 4.5 - - + +
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Residues in contact with GLY 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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201A VAL* 1.3 79.7 - - - +
203A TRP* 1.3 77.1 + - - -
292A PRO* 3.3 6.1 - - - +
293A VAL* 3.0 27.8 + - - -
444A GLU 3.5 7.0 - - - -
445A ILE* 3.0 14.3 - - - +
446A PRO* 5.2 0.4 - - - -
135B TYR* 5.7 0.2 + - - -
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Residues in contact with TRP 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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202A GLY* 1.3 82.6 - - - -
204A ALA* 1.3 61.0 + - - +
205A VAL* 4.2 1.6 - - + -
290A LYS* 3.5 61.0 - - + +
291A ILE 3.3 5.6 - - - +
292A PRO* 3.6 40.8 - - + -
293A VAL* 4.2 4.3 - - - -
420A VAL* 4.8 11.9 - - + -
443A LEU* 3.4 4.4 - - - +
444A GLU* 2.7 53.1 + - + +
445A ILE* 3.0 11.2 - - - +
134B GLN* 4.6 9.9 - - - -
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Residues in contact with ALA 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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203A TRP* 1.3 74.7 - - - +
205A VAL* 1.3 61.1 + - - +
217A VAL* 5.3 4.0 - - + -
283A PRO* 5.5 0.2 - - + -
285A VAL* 4.6 1.9 - - - +
290A LYS* 3.0 23.4 - - - -
291A ILE* 3.0 29.8 + - + +
293A VAL* 4.1 7.4 - - + +
441A LEU* 4.2 22.4 - - + -
442A ARG 3.3 6.3 - - - +
443A LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 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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203A TRP* 4.6 2.0 - - + -
204A ALA* 1.3 73.9 - - - +
206A ASN* 1.3 62.7 + - - +
207A ASP* 3.6 26.7 + - - +
289A SER 3.5 2.2 - - - +
290A LYS* 3.5 28.0 - - + -
422A LEU* 3.3 29.2 - - + -
441A LEU* 3.1 13.1 - - - +
442A ARG* 2.6 47.9 + - + +
444A GLU* 4.3 24.9 - - + +
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Residues in contact with ASN 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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205A VAL* 1.3 75.3 - - - +
207A ASP* 1.3 55.2 + - - +
208A SER* 3.0 14.2 + - - -
210A THR 3.0 13.9 + - - +
211A PRO* 3.6 0.2 - - - +
212A GLN* 3.4 21.6 - - - +
285A VAL* 3.2 33.7 + - + -
286A PRO 4.0 0.7 - - - +
287A ALA* 2.8 40.0 - - - +
288A ARG* 2.8 35.0 + - - -
289A SER 2.8 9.5 + - - +
441A LEU* 3.9 7.7 + - + +
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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