Contacts of the strand formed by residues 626 - 631 (chain B) in PDB entry 6A5T
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 626 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394B PHE* 3.3 33.1 + - + +
397B LYS 5.3 2.5 + - - +
398B ARG* 5.3 2.0 - - - +
399B LEU* 4.0 29.6 - - + +
514B LEU* 4.0 34.3 - - + +
532B LEU* 4.6 7.6 - - + -
536B SER* 5.0 3.1 - - - -
538B ILE* 4.1 15.7 - - + -
624B GLY 4.4 3.1 - - - +
625B ARG* 1.3 73.0 - - - +
627B TYR* 1.3 70.4 + - - +
691B ASP* 3.2 3.5 - - - +
692B GLY* 3.2 24.6 + - - +
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Residues in contact with TYR 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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28B LYS* 4.6 6.5 + - - -
514B LEU* 4.0 8.5 - - - -
535B LEU 3.3 2.6 - - - +
536B SER* 3.4 4.0 - - - -
537B GLY* 2.6 72.1 + - - -
538B ILE 4.2 4.3 + - - -
539B SER* 3.8 16.4 - - - -
605B GLU* 3.1 43.0 + - + +
625B ARG* 4.2 11.7 - - - -
626B VAL* 1.3 79.6 - - - +
628B ARG* 1.3 62.2 + - - +
629B PRO* 5.9 0.2 - - + -
689B TYR* 3.2 46.7 - + + -
690B VAL 3.1 17.5 - - - +
691B ASP* 3.5 11.4 - - + +
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Residues in contact with ARG 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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512B TRP* 3.2 34.4 + - - -
513B GLY* 3.0 28.6 - - - +
514B LEU* 3.8 6.5 - - + +
535B LEU* 3.2 21.1 - - + +
627B TYR* 1.3 80.4 - - - +
629B PRO* 1.3 70.1 + - + +
630B LEU* 3.3 21.4 - - - +
689B TYR* 3.6 1.4 - - - -
690B VAL* 2.8 38.4 + - + +
695B GLU* 2.2 34.4 + - - -
700B ILE* 3.8 10.1 - - - +
742B GLU* 2.4 31.4 + - - -
747B MET 5.8 2.2 - - - -
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Residues in contact with PRO 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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24B PHE* 5.1 3.6 - - + -
535B LEU* 3.6 37.0 - - + +
627B TYR* 5.5 0.4 - - + -
628B ARG* 1.3 96.3 + - + +
630B LEU* 1.3 79.3 + - - +
678B TRP* 4.3 17.5 - - + -
687B ILE* 3.7 17.3 - - + -
688B GLU 3.4 7.2 - - - +
689B TYR* 3.9 22.7 - - + -
743B ILE* 4.7 8.1 - - + +
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Residues in contact with LEU 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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628B ARG* 3.3 22.0 - - - +
629B PRO* 1.3 88.0 - - - +
631B PHE* 1.3 69.5 + - - +
632B ILE* 4.3 0.2 - - - +
687B ILE* 3.0 10.1 - - - +
688B GLU* 2.9 33.9 + - - +
690B VAL* 3.7 25.6 - - + -
698B ILE* 4.6 1.8 - - + -
700B ILE* 4.0 22.2 - - + -
740B HIS* 4.0 25.1 - - + -
741B CYS 4.4 1.6 - - - +
742B GLU* 3.5 31.6 - - + +
743B ILE* 4.7 6.3 - - - +
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Residues in contact with PHE 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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12B ILE* 5.3 3.8 - - + -
17B CYS* 4.0 18.8 - - - -
20B VAL* 4.4 19.5 - - + -
630B LEU* 1.3 79.9 - - - +
632B ILE* 1.3 61.8 + - - +
633B VAL 3.5 1.9 + - - -
645B LEU* 3.5 32.1 - - + -
647B ILE* 4.4 17.5 - - + -
686B VAL 3.7 4.9 - - - +
687B ILE* 3.9 23.3 - - + -
704B PRO* 4.9 3.1 - - + -
740B HIS* 3.6 12.5 - - - -
741B CYS 3.2 30.1 + - - +
742B GLU 3.7 19.7 - - - -
743B ILE* 3.3 39.2 - - + +
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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