Contacts of the strand formed by residues 626 - 634 (chain B) in PDB entry 3N56
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 GLY 626 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578B PHE 3.3 5.8 - - - -
580B SER* 4.2 6.1 - - - -
583B ALA* 3.3 23.5 - - - +
622B ASN* 3.4 5.8 - - - +
623B THR* 2.5 42.8 + - - +
625B TYR* 1.3 80.5 - - - +
627B MET* 1.3 59.2 + - - -
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Residues in contact with MET 627 (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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577B GLU* 3.7 6.6 - - - +
578B PHE* 2.8 73.6 + - + +
583B ALA* 5.8 0.4 - - + -
593B ALA* 6.2 2.5 - - + -
596B TYR* 4.1 15.3 - - - -
597B LEU* 4.0 36.1 - - + -
620B LEU* 5.0 2.7 - - + -
621B GLN 3.7 4.0 - - - -
622B ASN* 4.3 1.6 - - + +
623B THR* 4.4 2.7 - - - -
626B GLY* 1.3 79.5 - - - +
628B TYR* 1.3 62.2 + - - +
649B MET* 4.3 16.2 - - - +
719B LEU* 4.2 15.0 - - + -
720B LEU* 4.1 23.6 - - + -
723B LEU* 4.7 6.3 - - + -
749B LEU* 6.4 0.2 - - + -
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Residues in contact with TYR 628 (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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575B ASN* 3.7 12.8 + - - -
576B PHE 3.6 8.7 - - - -
577B GLU* 4.0 7.6 - - - +
578B PHE* 4.9 0.2 - - - -
619B ASP* 4.1 20.9 + - - -
620B LEU* 3.4 9.6 - - - +
621B GLN* 2.8 54.4 + - + +
623B THR* 3.8 17.0 - - + -
627B MET* 1.3 75.1 - - - +
629B LEU* 1.3 71.8 + - - +
630B SER* 3.3 29.0 + - - -
632B LYS* 4.6 5.5 + - - -
908B TRP* 3.6 38.3 + + - -
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Residues in contact with LEU 629 (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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574B LEU 3.6 1.7 - - - +
575B ASN* 3.6 1.6 - - - -
576B PHE* 2.8 49.0 + - + +
578B PHE* 3.9 16.8 - - + -
618B TYR* 4.0 15.3 - - + -
619B ASP 3.4 13.7 - - - +
620B LEU* 3.8 24.5 - - + -
628B TYR* 1.3 78.3 - - - +
630B SER* 1.3 64.5 + - - +
631B VAL* 4.5 5.2 - - + -
642B LEU* 3.8 15.9 - - + -
645B ILE* 4.2 12.6 - - + -
646B ILE* 3.7 29.8 - - + -
649B MET* 4.1 8.3 - - + -
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Residues in contact with SER 630 (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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574B LEU 3.4 3.1 - - - -
575B ASN* 3.1 20.8 + - - -
618B TYR* 3.2 5.7 - - - +
619B ASP* 2.9 42.0 + - - +
628B TYR* 3.3 25.3 + - - -
629B LEU* 1.3 74.4 - - - +
631B VAL* 1.3 65.5 + - - +
632B LYS* 3.3 27.1 + - - +
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Residues in contact with VAL 631 (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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573B ASN* 3.6 1.6 - - - -
574B LEU* 2.8 52.6 + - + +
576B PHE* 5.3 0.4 - - + -
616B LEU* 4.4 7.6 - - + -
617B SER 3.4 9.6 - - - +
618B TYR* 4.2 11.0 - - + -
629B LEU* 4.5 7.0 - - + -
630B SER* 1.3 79.4 - - - +
632B LYS* 1.3 61.7 + - - +
638B GLN* 3.7 34.6 - - + +
641B LEU* 4.4 9.4 - - + -
642B LEU* 4.2 24.9 - - + -
645B ILE* 4.4 10.3 - - + -
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Residues in contact with LYS 632 (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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572B ALA 3.6 5.2 - - - -
573B ASN* 3.3 24.3 + - + +
575B ASN* 4.2 12.1 + - - +
616B LEU* 3.7 4.4 - - - +
617B SER* 2.8 43.5 + - - +
619B ASP* 5.8 4.9 - - - -
628B TYR* 4.6 4.4 + - - -
630B SER* 3.3 27.4 + - - +
631B VAL* 1.3 77.9 - - - +
633B GLY* 1.3 58.0 + - - +
638B GLN* 4.1 2.7 - - - -
901B SER* 4.7 17.2 + - - -
904B SER* 5.5 3.4 - - - -
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Residues in contact with GLY 633 (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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571B LYS* 3.1 15.1 - - - +
572B ALA 2.9 32.2 + - - +
573B ASN* 4.5 0.8 + - - -
615B GLY 3.2 13.2 - - - -
616B LEU* 4.5 1.6 - - - -
632B LYS* 1.3 75.9 - - - +
634B TYR* 1.3 64.4 + - - -
638B GLN* 3.5 2.5 - - - +
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Residues in contact with TYR 634 (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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417B LEU* 6.3 1.1 - - + -
420B VAL* 3.4 30.7 + - + +
421B ALA* 3.6 21.0 + - - +
424B PHE* 4.2 15.2 + + + +
532B PRO* 3.7 28.9 - - + -
535B PHE* 4.4 6.3 - + + -
570B PRO* 3.2 26.7 - - + +
571B LYS* 4.1 25.6 + - + -
614B ALA 3.3 28.0 - - - -
615B GLY* 3.3 20.1 + - - -
616B LEU* 3.7 19.9 - - + +
633B GLY* 1.3 71.2 - - - -
635B ASN* 1.3 64.3 + - - +
636B ASP* 3.3 2.8 + - + +
637B LYS 3.9 5.0 + - - -
638B GLN* 4.0 0.6 - - - +
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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