Contacts of the strand formed by residues 629 - 636 (chain A) in PDB entry 6EJ9
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 SER 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A GLN* 3.3 16.7 + - - +
626A GLY* 3.2 20.3 + - - +
627A LEU 4.4 0.5 - - - +
628A ARG* 1.3 78.6 + - - +
630A TYR* 1.3 62.4 + - - +
631A TRP* 3.5 35.7 - - - -
689A TYR* 4.3 8.5 + - - -
690A PHE 3.3 11.2 - - - -
691A LEU* 3.6 16.9 - - - +
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Residues in contact with TYR 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ALA* 3.4 24.1 - - - +
340A ARG* 4.1 17.6 + - + -
341A GLN* 4.1 11.9 + - + +
602A ALA* 3.7 28.8 - - + +
603A VAL* 3.7 17.7 - - + -
606A GLN* 3.6 24.7 - - + +
629A SER* 1.3 76.8 - - - +
631A TRP* 1.3 82.2 + - - +
632A GLU* 2.7 40.2 + - + +
688A LEU 3.7 0.7 - - - +
689A TYR* 3.6 4.5 - - - -
690A PHE* 2.9 51.6 + + + +
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Residues in contact with TRP 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ARG* 3.2 65.0 + - - +
626A GLY* 4.4 19.5 - - - -
629A SER* 3.5 30.1 - - - -
630A TYR* 1.3 90.4 + - - +
632A GLU* 1.3 61.7 + - - +
633A ASN 4.3 0.2 - - - -
687A HIS* 4.4 10.5 - + + -
688A LEU 3.4 7.0 - - - +
689A TYR* 3.6 29.3 - + - -
699A LEU* 3.6 29.3 - - + +
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Residues in contact with GLU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.7 31.3 + - + +
338A ALA* 3.4 17.8 - - - +
339A SER 6.3 0.2 - - - +
603A VAL* 3.5 21.2 - - - +
630A TYR* 2.7 37.3 + - + +
631A TRP* 1.3 74.8 - - - +
633A ASN* 1.3 63.7 + - - +
634A VAL* 3.5 3.4 + - + +
687A HIS* 3.8 5.1 - - - -
688A LEU* 2.8 55.7 + - + +
756A PHE* 5.9 0.7 - - - -
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Residues in contact with ASN 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 2.8 59.9 + - - +
339A SER* 5.7 0.6 + - - -
366A TYR* 3.3 37.5 + - + +
632A GLU* 1.3 71.0 - - - +
634A VAL* 1.3 58.4 + - - +
635A TYR 3.1 26.5 + - - +
636A ASP* 3.5 17.9 + - - +
685A SER* 4.1 2.2 - - - -
686A VAL 3.5 5.8 - - - -
687A HIS* 3.5 31.7 + - - +
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Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.6 23.9 + - + +
632A GLU* 3.9 4.9 - - + +
633A ASN* 1.3 78.0 - - - +
635A TYR* 1.3 62.4 + - - +
644A LEU* 5.0 3.5 - - - +
652A TYR* 4.0 13.6 + - - +
686A VAL* 2.9 35.5 + - + +
688A LEU* 3.7 42.8 - - + +
698A PHE* 4.7 2.0 - - + -
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Residues in contact with TYR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 4.0 2.7 - - - +
633A ASN* 3.1 12.4 + - - +
634A VAL* 1.3 80.8 - - - +
636A ASP* 1.3 75.1 + - - +
637A GLU* 3.8 17.2 + - - +
639A ASP* 5.4 0.9 - - + -
640A GLY* 3.3 42.3 + - - -
641A ILE* 3.4 11.0 + - + +
643A SER* 3.8 8.7 - - - -
644A LEU* 3.6 44.6 - - + -
652A TYR* 4.5 1.3 - - + -
683A PRO* 3.5 29.3 + - + -
685A SER* 3.2 11.7 - - - -
686A VAL* 2.9 45.9 + - + -
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Residues in contact with ASP 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 4.2 2.9 - - - +
366A TYR* 3.7 25.3 - - + -
369A ARG* 2.8 32.9 + - - +
370A GLN* 5.4 0.9 - - - +
633A ASN* 3.5 13.8 + - - +
635A TYR* 1.3 83.3 - - - +
637A GLU* 1.3 69.0 + - - +
638A PRO* 3.3 12.5 - - - +
639A ASP* 3.0 25.3 + - - +
684A ALA 4.0 2.4 - - - +
685A SER* 4.0 8.8 - - - -
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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