Contacts of the strand formed by residues 684 - 693 (chain D) in PDB entry 5GG4
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 ASP 684 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A ILE* 3.9 26.4 - - - +
678D LYS 4.2 0.5 - - - +
679D PHE* 3.6 19.5 - - + -
680D ASP* 2.8 42.5 + - - +
683D HIS* 1.3 80.9 - - - +
685D VAL* 1.3 61.3 + - - +
706D TYR* 5.5 0.2 - - + -
707D THR 3.4 11.0 - - - +
708D PRO* 3.6 20.7 - - - +
709D ILE* 4.0 1.6 - - - -
623H LYS* 2.9 28.2 + - - -
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Residues in contact with VAL 685 (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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679D PHE* 3.9 4.7 - - - -
684D ASP* 1.3 76.4 - - - +
686D MET* 1.3 68.5 + - - +
687D LEU* 4.1 11.9 - - + -
705D ILE 3.5 1.7 - - - +
706D TYR* 3.7 1.2 - - - -
707D THR* 2.7 53.7 + - + +
709D ILE* 4.1 12.6 - - + -
753D LEU* 4.0 15.9 - - + -
760D LEU* 4.3 10.3 - - + -
761D MET 3.7 26.0 - - - +
762D ASP* 3.3 13.5 - - - +
623H LYS* 3.9 10.5 - - + -
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Residues in contact with MET 686 (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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623D TRP* 3.5 65.5 - - + -
635D PRO* 4.3 7.0 - - + -
661D PHE* 4.7 3.1 - - + -
663D GLU* 4.5 0.9 - - - +
679D PHE* 4.0 0.2 - - - -
685D VAL* 1.3 72.5 - - - +
687D LEU* 1.3 59.5 + - - +
688D PHE* 3.4 32.8 - - + -
704D HIS* 4.0 33.2 - - + -
705D ILE 3.4 6.3 - - - +
706D TYR* 4.1 12.3 - - + -
762D ASP* 3.0 12.9 + - + +
763D GLY* 2.8 36.3 + - - +
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Residues in contact with LEU 687 (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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685D VAL* 4.1 21.8 - - + -
686D MET* 1.3 75.9 - - - +
688D PHE* 1.3 66.3 + - - +
689D LEU* 4.3 4.0 + - + -
704D HIS* 3.1 5.4 - - - +
705D ILE* 3.0 40.3 + - + +
707D THR* 4.0 22.0 - - + -
716D LEU* 4.0 20.6 - - + -
753D LEU* 4.1 13.7 - - + -
757D LEU* 4.2 15.9 - - + -
760D LEU* 4.3 4.0 - - + -
764D ASP* 3.5 30.1 - - + +
766D ILE* 4.7 12.8 - - + -
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Residues in contact with PHE 688 (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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575D PHE* 3.8 17.0 - + - -
583D MET* 4.1 15.5 - - + -
635D PRO* 3.4 33.4 - - + -
661D PHE* 3.8 16.8 - + - -
686D MET* 3.4 28.5 - - + -
687D LEU* 1.3 77.1 - - - +
689D LEU* 1.3 63.8 + - - +
690D LYS* 6.1 0.7 - - + -
701D TYR* 3.5 32.3 - + + -
703D GLY 3.7 2.5 - - - +
704D HIS* 3.8 11.9 - - + -
763D GLY* 3.8 17.3 - - - -
764D ASP 2.9 10.5 + - - +
765D ILE* 3.3 18.4 - - + +
766D ILE* 3.1 25.6 + - - +
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Residues in contact with LEU 689 (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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687D LEU* 4.9 3.4 - - + +
688D PHE* 1.3 77.8 - - - +
690D LYS* 1.3 65.7 + - - +
701D TYR* 3.6 3.6 - - - -
702D CYS* 3.0 38.4 + - + +
703D GLY 3.0 11.5 + - - +
705D ILE* 4.1 34.3 - - + -
719D VAL* 4.6 2.9 - - + -
720D MET* 4.0 28.5 - - + -
723D ARG* 4.0 26.7 - - - +
766D ILE* 3.5 36.6 - - + +
768D PHE* 4.3 4.9 - - + -
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Residues in contact with LYS 690 (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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578D HIS* 5.4 7.0 - - - -
580D GLY 3.9 12.4 + - - -
582D ASP 2.5 35.4 + - - +
583D MET* 5.0 4.9 - - - +
688D PHE* 6.1 0.9 - - + -
689D LEU* 1.3 80.3 - - - +
691D MET* 1.3 62.4 + - - +
699D LEU* 5.2 11.4 - - + -
700D ASN 3.7 7.2 - - - +
701D TYR* 4.5 18.8 - - + -
702D CYS 4.4 0.4 - - - +
737D GLU* 3.0 23.4 + - - +
765D ILE* 3.8 18.3 - - + +
766D ILE 3.4 4.9 + - - -
767D VAL* 3.2 21.3 - - + -
768D PHE* 2.9 31.4 + - - -
787D PHE* 5.1 5.4 - - + -
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Residues in contact with MET 691 (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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690D LYS* 1.3 74.1 - - - +
692D TYR* 1.3 82.8 + - - +
693D ASP* 3.9 16.8 - - + +
694D PRO* 5.8 0.4 - - + -
699D LEU* 3.4 1.8 - - - -
700D ASN* 2.7 61.2 + - + +
702D CYS* 3.8 9.2 - - - -
724D ALA* 4.1 9.2 - - + -
726D PHE* 3.4 33.0 - - + -
767D VAL* 4.7 0.4 - - - -
768D PHE* 3.4 33.2 - - + +
769D GLN* 4.4 4.7 - - - -
770D LYS* 4.9 1.1 - - + +
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Residues in contact with TYR 692 (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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690D LYS 4.1 0.8 + - - -
691D MET* 1.3 86.4 - - - +
693D ASP* 1.3 69.9 - - - +
694D PRO* 3.4 13.7 - - + +
697D ARG* 3.6 32.0 - - - -
698D SER 3.3 11.4 - - - -
699D LEU* 4.2 7.0 - - + +
767D VAL* 3.9 7.8 - - + +
768D PHE 2.9 9.1 + - - +
769D GLN* 3.4 26.1 - - - +
780D LEU* 2.8 39.6 + - - +
782D THR 3.3 21.1 - - - -
783D ALA* 3.3 35.9 - - + -
786D TYR* 3.6 27.4 - + + +
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Residues in contact with ASP 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D MET* 3.9 16.6 - - - +
692D TYR* 1.3 74.7 - - - +
694D PRO* 1.3 58.5 - - - +
695D LYS* 3.6 13.5 + - - +
696D THR* 2.7 38.4 + - - +
697D ARG* 2.7 31.9 + - - -
698D SER 2.8 19.4 + - - +
700D ASN* 4.2 6.2 - - - +
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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