Contacts of the strand formed by residues 313 - 319 (chain D) in PDB entry 6CCV
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 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D ALA* 5.8 1.6 + - - +
100D PRO* 5.1 6.3 - - + -
101D VAL 3.4 7.4 - - - +
102D THR* 4.4 14.6 - - + -
114D LEU* 5.4 1.6 - - + -
258D ALA* 4.7 2.9 - - + +
261D ILE* 4.3 23.6 - - + -
262D LYS* 4.0 26.7 - - + +
265D ILE* 4.8 7.4 - - + -
310D MET* 3.0 43.3 - - + +
311D GLY* 3.7 3.8 - - - +
312D MET* 1.3 83.3 - - + +
314D LEU* 1.3 65.4 + - - +
315D ASP* 3.8 5.0 + - - +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123C CYS* 4.0 21.8 - - + -
15D ALA 5.2 3.6 - - - +
17D ALA* 5.8 0.7 - - - -
20D ILE* 5.1 1.8 - - + -
97D LEU* 3.6 13.5 - - + +
100D PRO* 3.6 6.7 - - - +
101D VAL* 2.8 35.3 + - + +
103D HIS* 4.0 25.6 - - + -
311D GLY 3.4 24.0 - - - +
313D VAL* 1.3 74.6 - - - +
315D ASP* 1.3 60.8 + - - +
316D ALA 3.9 14.6 - - - +
317D VAL* 4.7 2.2 - - + -
378D VAL* 4.7 10.3 - - + -
382D PHE* 3.6 33.2 - - + -
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Residues in contact with ASP 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 3.8 23.7 - - + +
21D ARG* 3.8 13.1 + - - +
96D GLU* 3.4 7.0 - - - +
97D LEU* 3.1 33.9 + - - +
99D ALA 5.6 0.2 - - - -
100D PRO* 4.0 17.8 - - - +
262D LYS* 3.2 34.0 + - - +
310D MET* 5.3 2.6 - - - +
313D VAL* 3.8 5.8 + - - +
314D LEU* 1.3 74.8 - - - +
316D ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 4.3 7.7 - - + +
20D ILE* 3.3 29.4 - - + +
21D ARG* 4.3 13.7 - - + +
94D HIS* 4.2 13.0 - - + -
95D ILE 3.1 13.5 - - - +
96D GLU* 3.9 18.4 - - - +
97D LEU* 4.5 0.9 - - - -
314D LEU* 3.9 10.6 - - - +
315D ASP* 1.3 78.6 + - - +
317D VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123C CYS* 5.3 0.4 - - - -
20D ILE* 4.0 2.2 - - - -
94D HIS* 3.1 2.4 - - - -
95D ILE* 2.8 46.5 + - + +
97D LEU* 3.6 33.7 - - + -
314D LEU* 4.7 7.0 - - + -
316D ALA* 1.3 77.0 - - - +
318D PRO* 1.3 79.6 - - + +
344D TYR* 5.1 2.0 - - + -
347D VAL* 5.3 2.7 - - + -
378D VAL* 4.5 18.4 - - + -
381D LEU* 4.1 13.5 - - + -
382D PHE* 3.9 23.3 - - + -
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Residues in contact with PRO 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C GLN 3.7 24.0 - - - +
1121C SER* 3.8 20.7 - - - +
1123C CYS* 3.7 22.0 - - - -
20D ILE* 3.6 26.2 - - + +
23D TRP* 4.7 8.3 - - + -
92D MET* 4.7 8.3 - - + -
93D GLY 3.5 8.3 - - - +
317D VAL* 1.3 95.7 - - + +
319D VAL* 1.3 59.7 + - - +
344D TYR* 3.3 18.2 + - - -
381D LEU* 5.2 0.3 - - - +
382D PHE* 5.5 0.2 - - - -
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Residues in contact with VAL 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121C SER* 4.8 0.9 - - - -
28D VAL* 3.4 24.2 - - + -
46D LEU* 4.1 15.3 - - + -
52D PHE* 4.1 6.7 - - + -
92D MET* 3.3 11.5 - - - +
93D GLY* 2.8 38.5 + - - -
94D HIS 3.7 7.0 - - - +
95D ILE* 3.6 24.5 - - + -
318D PRO* 1.3 77.3 - - - +
320D ILE* 1.3 72.4 + - - +
325D ARG* 4.0 17.5 - - - +
344D TYR* 3.7 15.9 - - + -
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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