Contacts of the strand formed by residues 308 - 313 (chain B) in PDB entry 1YHQ
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 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 4.7 3.1 - - + +
23B THR* 3.4 43.5 - - + +
24B PRO* 3.9 19.6 - - + +
42B ALA* 3.9 18.8 - - + -
43B GLY 3.5 16.8 - - - +
44B TYR* 3.9 29.5 - - + -
146B THR* 4.0 9.6 - - + -
156B LYS* 5.4 2.0 - - - +
160B ASP* 3.6 15.3 - - + +
162B MET* 3.6 14.4 - - + -
204B GLY* 4.5 1.2 - - - -
306B LYS 3.7 1.6 + - - -
307B ARG* 1.3 86.1 - - + +
309B VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.3 5.7 - - - +
43B GLY 2.9 41.8 + - - +
45B LYS* 4.5 9.4 - - + +
74B ILE* 3.6 35.0 - - + -
202B VAL* 4.1 7.6 - - + -
203B ALA 3.5 11.4 - - - +
204B GLY* 5.0 0.7 - - - -
301B VAL* 3.5 25.8 - - + -
302B PRO 3.8 11.2 - - - +
307B ARG* 4.1 9.2 - - + +
308B LEU* 1.3 79.9 - - - +
310B ARG* 1.3 62.4 + - - +
311B PHE* 4.3 6.5 - - + -
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PRO* 3.4 23.1 + - + -
26B PHE* 3.4 44.7 - - + +
29B TRP* 4.1 3.2 - - - -
40B GLY* 5.9 0.2 - - - -
41B PHE 3.5 11.5 - - - +
42B ALA* 4.2 0.7 - - + -
162B MET* 3.0 55.6 - - + +
163B GLU 3.4 10.3 + - - -
164B THR* 3.2 19.8 + - - +
202B VAL* 3.2 8.3 - - - +
203B ALA* 3.0 38.2 + - + +
309B VAL* 1.3 75.1 - - - +
311B PHE* 1.3 60.9 + - - +
8987B SR 2.4 40.8 - - - -
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.7 5.3 - - - -
40B GLY* 3.2 5.7 - - - -
41B PHE 2.8 37.7 + - - +
42B ALA* 4.1 5.2 - - - -
43B GLY 4.1 11.4 - - - -
74B ILE* 3.5 33.2 - - + -
76B THR* 3.5 24.9 - - + -
190B MET* 4.1 11.9 - - + -
194B PHE* 3.8 22.4 - - + -
200B ALA* 4.6 3.4 - - + -
201B ASP 3.6 2.2 - - - -
202B VAL* 4.2 16.8 - - + -
269B LEU* 4.3 17.3 - - + -
295B THR* 4.5 6.3 - - + -
297B VAL* 3.7 25.4 - - + -
309B VAL* 4.3 4.9 - - + -
310B ARG* 1.3 76.2 - - - +
312B ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28060 C 4.5 0.4 + - - -
28070 U 2.6 30.3 + - - -
26B PHE* 3.3 40.7 - - + +
27B ASN 4.4 1.4 - - - +
28B SER* 2.9 30.2 + - - +
29B TRP* 4.8 2.5 - - + -
30B PRO* 4.1 12.1 - - + -
39B GLN 3.9 6.5 - - - +
194B PHE* 3.7 4.0 - - - -
200B ALA* 3.2 3.5 - - - -
201B ASP* 2.7 84.2 + - - +
263B THR* 4.1 8.6 + - - +
265B LEU* 4.7 2.0 - - - +
311B PHE* 1.3 78.4 - - - +
313B PRO* 1.3 81.7 - - + +
314B ALA 3.1 0.3 + - - -
315B VAL* 3.5 19.9 - - - +
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Residues in contact with PRO 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.4 23.9 - - + +
39B GLN* 3.2 31.0 - - + +
193B ILE* 4.8 8.5 - - + +
194B PHE* 3.7 23.3 - - + -
199B TYR 4.0 2.9 - - - +
312B ARG* 1.3 95.8 - - + +
314B ALA* 1.3 70.3 + - - +
315B VAL 3.1 2.8 + - - -
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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