Contacts of the strand formed by residues 647 - 652 (chain B) in PDB entry 3U11
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 ASN 647 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644B THR* 3.5 21.7 - - + +
645B LYS 3.6 1.3 - - - +
646B GLY* 1.3 76.7 - - - +
648B LYS* 1.3 73.9 + - - +
649B GLU* 2.2 42.5 + - - +
713B ARG 4.1 1.0 - - - +
714B ILE* 2.2 59.3 + - - +
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Residues in contact with LYS 648 (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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647B ASN* 1.3 82.7 + - - +
649B GLU* 1.3 87.8 + - - +
650B THR* 3.6 1.4 + - - -
713B ARG* 2.5 60.5 - - - +
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Residues in contact with GLU 649 (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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642B VAL* 2.3 38.1 - - + +
643B LEU* 3.3 31.1 - - - +
644B THR* 2.7 36.3 + - - +
647B ASN* 2.2 30.5 + - - +
648B LYS* 1.3 101.3 - - - +
650B THR* 1.3 74.5 + - - +
714B ILE* 4.9 10.7 - - + +
846B CMP 4.7 2.7 + - - -
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Residues in contact with THR 650 (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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641B SER* 3.5 1.4 - - - -
642B VAL* 2.9 27.5 + - - +
648B LYS 3.6 3.5 + - - -
649B GLU* 1.3 96.8 + - - +
651B LYS* 1.3 82.8 + - - +
652B LEU* 5.1 4.5 - - + -
713B ARG* 5.1 9.5 + - - +
846B CMP 3.5 32.6 + - + +
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Residues in contact with LYS 651 (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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639B VAL* 4.3 13.5 - - + -
640B VAL 3.0 8.7 - - - +
641B SER* 2.6 37.5 + - - +
643B LEU* 5.6 2.4 - - - +
650B THR* 1.3 87.4 - - - +
652B LEU* 1.3 66.0 + - - +
653B ALA* 4.2 0.5 + - - +
674B ARG* 4.8 5.3 - - - +
676B ASP* 3.5 11.2 - - - +
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Residues in contact with LEU 652 (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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635B ILE* 3.9 16.0 - - + +
639B VAL* 3.5 3.8 - - - +
640B VAL* 2.9 34.0 + - + +
642B VAL* 3.8 18.6 - - + +
650B THR* 5.1 5.4 - - + -
651B LYS* 1.3 80.1 - - - +
653B ALA* 1.3 60.7 + - - +
656B SER* 3.9 15.5 - - - +
657B TYR 3.9 11.2 - - - +
658B PHE* 4.0 16.6 - - + -
710B ARG* 3.7 28.9 - - - +
846B CMP 3.8 25.4 - - + +
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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