Contacts of the strand formed by residues 307 - 315 (chain B) in PDB entry 5XOU
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 GLU 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PHE* 4.0 1.8 - - - -
15B ALA* 2.9 45.2 + - + +
305B THR* 3.7 4.5 + - + +
306B PRO* 1.3 74.7 - - - +
308B ALA* 1.3 73.2 + - - +
309B VAL* 3.5 0.9 + - - -
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Residues in contact with ALA 308 (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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10B PHE* 3.9 27.3 - - + -
11B LEU 5.0 1.3 - - - +
13B ARG 3.7 2.0 - - - +
14B PHE* 3.5 32.8 - - + -
291B ARG* 3.7 20.0 - - - +
306B PRO 4.2 0.6 + - - -
307B GLU* 1.3 79.5 - - - +
309B VAL* 1.3 61.9 + - - +
310B ARG* 3.8 5.5 + - - +
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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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10B PHE* 3.2 5.8 - - - +
11B LEU* 2.9 43.1 + - + -
13B ARG* 3.1 40.1 + - + +
14B PHE 4.0 2.7 - - - +
15B ALA* 4.2 13.0 - - + +
164B LEU* 4.5 9.9 - - + -
307B GLU 4.3 1.1 - - - +
308B ALA* 1.3 73.4 - - - +
310B ARG* 1.3 73.3 + - - +
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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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8B GLU* 2.8 36.7 + - - +
9B VAL 3.1 8.1 - - - +
10B PHE* 3.6 41.6 - - + -
11B LEU* 5.2 0.4 - - - -
308B ALA 3.8 4.9 + - - +
309B VAL* 1.3 85.5 - - - +
311B ALA* 1.3 63.4 + - - +
584B VAL* 3.6 21.7 - - + +
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Residues in contact with ALA 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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8B GLU* 3.5 8.8 - - - +
9B VAL* 2.9 37.8 + - + +
11B LEU* 4.4 16.2 - - + -
310B ARG* 1.3 77.3 - - - +
312B GLN* 1.3 63.4 + - - +
594B VAL* 3.8 24.0 - - + -
595B PRO 5.1 1.8 - - - +
596B LEU* 4.7 5.8 - - + -
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Residues in contact with GLN 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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6B LYS* 3.4 46.7 - - + +
7B THR 3.6 2.9 - - - +
8B GLU* 4.0 19.8 + - - +
311B ALA* 1.3 75.0 - - - +
313B ALA* 1.3 61.0 + - - +
314B TYR* 3.8 20.1 + - + +
594B VAL* 3.6 16.3 - - - +
595B PRO* 3.8 16.8 + - + +
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Residues in contact with ALA 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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6B LYS* 3.7 1.2 - - - +
7B THR* 2.8 38.4 + - + +
9B VAL* 3.7 31.0 - - + -
311B ALA 3.5 0.2 + - - -
312B GLN* 1.3 74.3 - - - +
314B TYR* 1.3 71.6 + - - +
592B LEU* 3.7 15.7 - - + -
593B TYR 3.4 7.9 - - - +
594B VAL* 3.9 9.0 - - + -
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Residues in contact with TYR 314 (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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5B GLY 3.5 4.9 - - - +
6B LYS* 4.1 28.4 - - + +
312B GLN* 3.8 27.5 + - + +
313B ALA* 1.3 82.1 - - - +
315B ARG* 1.3 64.7 + - - +
316B LEU* 3.6 3.5 + - + -
592B LEU* 3.7 4.4 - - - -
593B TYR* 2.9 61.5 + + + +
595B PRO* 3.9 27.1 - - + -
629B GLU* 4.6 15.0 - - - +
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Residues in contact with ARG 315 (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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4B LEU* 3.1 41.4 - - - +
5B GLY* 3.1 20.7 + - - +
6B LYS 5.3 1.6 + - - -
7B THR* 4.0 26.6 + - + +
314B TYR* 1.3 73.1 - - - +
316B LEU* 1.3 64.2 + - - +
317B SER 4.0 0.2 + - - -
587B ARG 5.5 4.4 + - - -
589B ALA* 5.3 12.1 - - - +
591B GLY 3.8 4.7 - - - +
592B LEU* 4.5 8.5 - - + +
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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