Contacts of the strand formed by residues 627 - 633 (chain D) in PDB entry 3JW0
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 ARG 627 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659C TYR* 3.2 48.5 + - + -
590D LYS* 4.8 11.7 - - - +
596D ASN 3.9 15.3 + - - +
597D ARG* 3.2 13.4 - - - +
598D PHE 2.9 23.2 + - - -
625D LYS 3.9 0.6 + - - -
626D ALA* 1.3 72.2 - - - +
628D LEU* 1.3 72.7 + - - +
703D HIS* 4.2 8.5 - - + -
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Residues in contact with LEU 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597D ARG* 4.4 1.6 - - - -
598D PHE* 4.0 17.7 - - + +
600D MET* 5.6 2.9 - - - -
624D LEU 5.1 1.3 - - - +
626D ALA 3.3 4.3 + - - +
627D ARG* 1.3 87.4 + - - +
629D TRP* 1.3 60.5 + - - +
630D ILE* 3.7 13.8 - - + +
644D ALA* 3.5 29.6 - - + +
647D TRP* 4.4 14.4 - - + -
648D PHE* 3.6 28.5 - - + -
699D LEU* 4.2 27.1 - - + -
703D HIS* 4.2 25.4 + - + +
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Residues in contact with TRP 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891C ASN* 3.5 30.3 - - + -
895C GLU* 2.8 38.7 + - + -
597D ARG* 2.9 49.6 - - + +
598D PHE 2.9 15.9 + - - +
599D GLU* 3.1 46.1 - - + +
600D MET 2.9 26.5 + - - +
628D LEU* 1.3 74.3 - - - +
630D ILE* 1.3 70.9 + - - +
631D GLU* 3.7 16.8 + - + +
642D GLY 5.5 1.8 - - - -
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Residues in contact with ILE 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D MET* 3.7 15.5 - - + +
602D LEU* 5.1 2.2 - - + -
628D LEU* 3.7 33.2 - - + +
629D TRP* 1.3 85.1 - - - +
631D GLU* 1.3 69.6 + - - +
632D PHE* 4.0 35.0 - - + -
641D GLY* 3.9 0.7 - - - -
642D GLY* 3.0 39.3 + - - +
643D VAL 4.4 5.4 - - - +
644D ALA* 4.0 17.0 - - - +
647D TRP* 3.8 32.5 - - + -
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Residues in contact with GLU 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C ALA* 4.3 4.2 - - - +
895C GLU* 2.4 36.8 - - - +
599D GLU* 3.9 7.1 - - - +
600D MET 2.9 22.5 + - - +
601D LYS* 3.7 28.2 - - + +
602D LEU* 3.0 18.7 + - - +
629D TRP* 3.7 27.2 + - + +
630D ILE* 1.3 73.2 - - - +
632D PHE* 1.3 62.6 + - - +
639D ASP* 3.5 21.6 - - + +
640D TYR* 3.6 12.3 - - - +
641D GLY 3.7 9.7 + - - -
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Residues in contact with PHE 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D LYS* 6.1 0.2 - - - -
602D LEU* 3.4 35.4 - - + +
604D ARG* 3.7 46.4 - - + +
607D ILE* 4.5 9.2 - - + -
630D ILE* 4.0 18.4 - - + -
631D GLU* 1.3 73.4 - - - +
633D GLU* 1.3 62.4 + - - +
639D ASP* 3.1 2.0 - - - -
640D TYR* 2.9 63.7 + + + +
642D GLY* 4.0 22.0 - - - -
643D VAL 4.8 1.1 - - - -
646D GLU* 4.2 25.4 - - + -
647D TRP* 4.9 5.2 - + - -
650D LEU* 4.5 3.1 - - + -
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Residues in contact with GLU 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D LYS* 3.8 26.8 + - + +
602D LEU* 3.2 13.1 + - - +
603D HIS* 3.5 50.2 + - + +
604D ARG* 4.2 4.2 + - - +
631D GLU 4.3 0.2 + - - -
632D PHE* 1.3 73.0 - - - +
634D SER* 1.3 77.4 + - - +
635D GLU 3.8 1.6 + - - +
637D GLY 3.7 17.2 - - - +
638D LEU* 3.7 1.7 - - - -
639D ASP* 3.8 25.3 + - + +
640D TYR* 4.8 1.1 - - - -
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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