Contacts of the strand formed by residues 702 - 713 (chain M) in PDB entry 4G7Z
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 702 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569M VAL* 3.6 19.4 - - - +
570M PRO 3.3 23.8 - - - -
571M LEU* 4.1 3.8 - - - -
572M ILE* 4.2 4.3 - - - -
701M THR* 1.3 76.9 - - - +
703M ILE* 1.3 61.7 + - - +
704M HIS* 3.4 16.6 + - - -
830M LYS* 4.6 0.4 - - - -
831M ARG 2.7 35.9 + - - +
996M LYS* 3.3 25.8 + - - +
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Residues in contact with ILE 703 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K PHE* 3.5 44.2 - - + -
76K VAL* 4.3 12.1 - - + -
569M VAL* 5.5 0.5 - - - +
570M PRO 4.7 3.9 + - - +
572M ILE* 3.7 25.8 - - + +
628M PHE* 4.1 19.1 - - + -
635M THR* 4.3 0.5 - - - -
636M ALA* 3.4 36.0 + - + +
640M ARG* 6.2 0.9 - - - +
702M SER* 1.3 76.6 - - - +
704M HIS* 1.3 73.7 + - - +
705M ILE* 4.7 3.1 - - + -
828M ALA* 4.4 9.0 - - + -
829M GLN 3.4 6.5 - - - +
830M LYS* 4.4 10.1 - - + -
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Residues in contact with HIS 704 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569M VAL* 3.5 20.2 - - + +
633M GLN 5.3 0.2 + - - -
634M GLY 3.2 22.8 + - - +
635M THR* 4.2 7.5 - - + +
636M ALA 4.7 0.2 - - - +
702M SER* 3.4 22.2 + - - -
703M ILE* 1.3 82.4 + - - +
705M ILE* 1.3 64.2 + - - +
827M VAL 3.9 0.3 - - - +
828M ALA* 3.3 0.9 - - - -
829M GLN* 2.8 44.7 + - + +
831M ARG* 3.4 41.8 + - + +
998M TYR* 5.0 7.8 - + - -
1000M MET* 3.5 34.4 - - + +
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Residues in contact with ILE 705 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628M PHE* 3.7 26.7 - - + +
630M ARG* 2.9 50.5 + - + -
634M GLY* 3.2 18.3 + - - +
636M ALA* 3.7 33.0 - - + +
703M ILE* 4.7 4.7 - - + -
704M HIS* 1.3 73.7 - - - +
706M GLU* 1.3 68.6 + - - +
801M VAL* 4.9 5.2 - - + -
826M TYR* 4.0 18.2 - - + -
827M VAL 3.3 14.4 - - - +
828M ALA* 3.8 19.1 - - + -
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Residues in contact with GLU 706 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630M ARG* 3.2 21.4 + - - -
633M GLN 5.5 0.7 - - - +
634M GLY* 5.0 3.1 - - - -
704M HIS 4.0 1.0 + - - -
705M ILE* 1.3 78.6 - - - +
707M ARG* 1.3 72.4 + - - +
708M TYR* 3.6 41.2 - - + +
796M GLU* 4.5 4.7 - - - +
826M TYR 3.9 0.2 - - - -
827M VAL* 2.7 36.8 + - + +
829M GLN* 5.4 8.1 - - + +
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Residues in contact with ARG 707 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ARG 4.9 3.8 + - - -
87M ASP* 3.4 31.9 + - - -
131M GLY 4.6 9.7 + - - -
630M ARG* 3.5 33.0 + - - +
706M GLU* 1.3 87.2 - - - +
708M TYR* 1.3 72.4 + - - +
709M GLU* 3.0 26.9 + - - +
824M ARG* 3.3 19.2 - - - +
825M VAL 3.9 3.6 - - - -
826M TYR* 3.5 40.5 + - + +
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Residues in contact with TYR 708 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706M GLU* 3.6 39.2 - - + +
707M ARG* 1.3 78.7 - - - +
709M GLU* 1.3 61.1 + - - +
749M VAL* 6.5 0.2 - - + -
755M LEU* 3.6 30.5 - - + -
790M LEU* 4.0 16.1 - - + +
791M ARG 5.3 1.1 - - - -
792M VAL* 5.2 2.7 - - + -
793M PRO* 3.5 24.7 - - + -
796M GLU* 2.7 43.1 + - - +
797M GLY* 4.2 6.5 + - - -
823M VAL 4.0 0.2 - - - +
824M ARG* 3.4 5.2 - - - +
825M VAL* 3.0 40.0 + - + +
827M VAL* 4.0 18.4 - - + -
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Residues in contact with GLU 709 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ASP* 4.4 2.7 - - - +
707M ARG* 3.0 30.4 + - + +
708M TYR* 1.3 76.3 - - - +
710M ILE* 1.3 69.8 + - - +
711M GLU* 4.1 14.5 - - + +
790M LEU* 4.1 11.8 - - - +
822M VAL* 4.0 13.4 - - + +
823M VAL 3.5 5.6 - - - +
824M ARG* 3.5 32.8 + - + -
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Residues in contact with ILE 710 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709M GLU* 1.3 77.7 - - - +
711M GLU* 1.3 68.8 + - - +
722M ILE* 4.6 6.4 - - + +
756M VAL* 3.9 29.6 - - + +
758M ARG* 3.5 46.9 - - + +
788M THR 4.4 0.2 - - - +
790M LEU* 3.6 39.7 - - + +
822M VAL* 3.5 5.4 - - - +
823M VAL* 3.1 43.7 + - + +
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Residues in contact with GLU 711 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709M GLU* 4.1 14.0 - - + +
710M ILE* 1.3 81.4 - - - +
712M ALA* 1.3 59.7 + - - +
713M ARG* 3.4 26.5 + - + +
720M GLU* 3.5 2.4 - - - +
722M ILE* 5.4 0.9 - - - -
758M ARG* 2.6 35.1 + - - +
816M LYS* 5.3 7.1 - - - +
819M VAL* 3.4 26.0 - - + +
821M GLU 3.5 5.8 - - - +
822M VAL* 3.5 25.9 - - + +
532N GLY* 5.6 2.1 - - - -
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Residues in contact with ALA 712 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711M GLU* 1.3 72.8 - - - +
713M ARG* 1.3 60.6 + - - +
720M GLU* 3.2 32.1 - - + +
722M ILE* 4.0 15.4 - - + +
758M ARG* 4.5 3.6 - - - +
819M VAL* 3.8 1.2 - - - +
820M ARG* 2.8 25.7 + - + +
821M GLU* 3.0 35.3 + - + +
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Residues in contact with ARG 713 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711M GLU* 3.4 37.3 + - + +
712M ALA* 1.3 77.2 - - - +
714M ASP* 1.3 68.3 + - - +
715M THR* 3.5 2.7 + - - +
719M PRO* 4.0 0.2 - - - +
720M GLU* 2.9 63.4 + - - +
758M ARG* 3.6 16.0 - - - +
818M GLY 3.6 8.1 - - - +
819M VAL* 4.1 22.0 - - + -
820M ARG* 4.1 3.7 + - - +
531N ASP* 2.9 38.9 + - - -
532N GLY* 3.3 30.6 + - - -
533N GLY* 4.4 2.9 - - - +
309P LYS* 5.1 5.2 - - - +
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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