Contacts of the strand formed by residues 316 - 322 (chain A) in PDB entry 3KQG
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A SER* 3.3 12.6 - - - +
211A LEU* 3.6 34.1 - - - +
212A ILE 3.8 10.3 - - - -
213A PRO* 3.9 9.1 - - + +
249A LEU* 3.8 33.2 - - + -
250A ILE 3.7 7.4 + - - +
251A TYR* 3.0 31.9 - - + +
252A TRP* 2.7 21.3 + - - -
315A PHE* 1.3 78.0 - - - +
317A PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 317 (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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208A TYR* 3.3 2.6 - + - +
210A SER* 2.7 53.0 + - - -
212A ILE* 3.4 25.8 - - + -
214A LYS* 3.8 22.2 - - + -
219A ALA* 3.6 30.5 - - + -
222A PHE* 3.2 47.3 - + + -
223A CYS* 4.2 5.4 - - - -
230A LEU* 3.8 3.1 - - + -
251A TYR* 3.7 2.4 - - - -
252A TRP* 3.6 17.5 - - + +
315A PHE 4.0 5.4 - - - -
316A LEU* 1.3 77.5 - - - +
318A ILE* 1.3 65.4 + - - +
319A CYS* 3.8 17.0 - - - -
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Residues in contact with ILE 318 (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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207A TYR* 4.2 5.2 - - + -
208A TYR 3.1 6.3 - - - +
209A PHE* 3.5 35.2 - - + -
230A LEU* 3.4 9.8 - - - +
231A THR* 2.9 42.3 + - + +
242A LEU* 4.1 21.1 - - + +
246A ALA* 5.3 0.2 - - + -
251A TYR* 3.5 33.0 - - + -
252A TRP 3.1 8.6 + - - +
253A ILE* 4.3 10.5 - - + -
298A ILE* 4.8 9.4 - - + -
317A PHE* 1.3 78.5 - - - +
319A CYS* 1.3 72.9 + - - +
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Residues in contact with CYS 319 (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 TRP* 4.3 3.1 - - + -
207A TYR* 3.1 6.1 - - - -
208A TYR* 2.8 46.7 + - + +
222A PHE* 4.1 6.1 - - - -
223A CYS* 2.1 49.4 - - - -
226A ARG* 5.7 0.4 - - - -
228A SER* 3.8 14.1 - - - +
229A HIS 3.3 5.8 - - - -
317A PHE* 3.8 19.3 - - - -
318A ILE* 1.3 79.8 - - - +
320A LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 320 (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 ASN* 3.8 24.0 - - + +
206A PHE 3.3 8.1 - - - +
207A TYR* 3.7 17.5 - - + -
228A SER* 3.1 15.4 - - - -
229A HIS* 2.8 19.8 + - - +
231A THR* 3.3 23.8 - - - +
232A SER* 2.9 36.7 + - - +
234A THR* 4.4 5.9 + - - +
238A GLU* 2.7 34.2 + - - -
268A ASP* 4.4 7.4 - - - +
319A CYS* 1.3 76.1 - - - +
321A ARG* 1.3 65.3 + - - +
322A PRO* 5.7 0.7 - - + -
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Residues in contact with ARG 321 (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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194A VAL* 3.7 32.7 - - - +
199A TRP* 4.0 26.0 - - + -
205A ASN* 3.6 5.0 - - - -
206A PHE* 2.8 59.2 + - + +
226A ARG 4.0 11.8 + - - -
227A ASN* 3.6 31.1 - - - +
228A SER* 3.4 10.5 - - - -
320A LYS* 1.3 76.9 - - - +
322A PRO* 1.3 79.6 + - + +
323A TYR* 5.4 0.2 - - - +
324A VAL* 5.5 6.1 - - - +
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Residues in contact with PRO 322 (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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204A GLY 3.7 1.8 - - - +
205A ASN* 3.2 17.0 - - - +
206A PHE* 4.4 0.2 - - - -
227A ASN 5.6 0.2 - - - +
320A LYS* 4.9 1.1 - - + +
321A ARG* 1.3 103.4 + - + +
323A TYR* 1.3 66.2 + - - +
324A VAL* 3.3 12.8 + - + +
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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