Contacts of the strand formed by residues 987 - 996 (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 ILE 987 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675M ALA* 4.6 0.2 - - + -
676M ILE 3.3 26.2 - - - +
677M MET* 3.6 33.4 - - + -
971M LYS* 3.3 5.1 - - - -
972M VAL 2.9 30.9 + - - +
974M LEU* 4.1 23.3 - - + -
983M ILE* 3.5 30.5 - - + -
985M GLY 4.0 7.4 + - - +
986M PRO* 1.3 79.9 - - - +
988M VAL* 1.3 73.8 + - - +
989M VAL* 3.4 6.6 + - + +
946N GLY* 4.2 13.5 - - - +
948N THR* 4.0 4.0 - - - -
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Residues in contact with VAL 988 (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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675M ALA* 3.5 1.9 - - - -
676M ILE* 2.9 48.7 + - + +
885M ILE* 5.3 0.7 - - + -
888M THR* 4.4 9.6 - - + -
889M HIS* 3.4 27.8 - - + +
970M GLY 3.4 6.1 - - - +
971M LYS* 3.7 19.5 - - + -
987M ILE* 1.3 73.1 - - - +
989M VAL* 1.3 62.7 + - - +
948N THR* 3.2 20.9 + - - +
949N ILE 3.4 16.6 - - - +
950N GLY* 3.4 17.7 - - - +
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Residues in contact with VAL 989 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673M LEU* 4.3 12.1 - - + -
674M VAL 3.2 14.4 - - - +
675M ALA* 3.9 14.4 - - + -
861M LEU* 5.0 8.1 - - + -
867M VAL* 3.8 20.9 - - + -
888M THR* 3.7 8.6 - - - +
889M HIS* 5.1 0.3 + - - -
892M LEU* 3.3 29.7 - - + +
970M GLY 3.5 5.1 + - - +
972M VAL* 3.7 30.7 - - + +
974M LEU* 4.0 14.6 - - + -
987M ILE 3.4 5.6 + - - +
988M VAL* 1.3 81.4 - - - +
990M GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 990 (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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673M LEU* 3.7 12.1 - - - -
674M VAL* 2.9 36.9 + - - +
888M THR* 3.4 17.8 - - - +
892M LEU* 3.7 11.7 - - - -
989M VAL* 1.3 78.5 - - - +
991M GLN* 1.3 61.5 + - - -
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Residues in contact with GLN 991 (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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575M GLN* 5.8 0.6 - - - +
578M VAL* 3.5 28.6 - - + +
671M ASN* 4.0 24.6 + - + +
672M VAL 3.3 12.5 - - - +
673M LEU* 4.0 4.5 - - + +
887M GLU* 3.1 25.1 - - - +
888M THR* 3.6 2.9 - - - -
891M GLY* 3.4 24.0 + - - +
894M GLY 4.3 1.6 - - - +
895M TYR* 3.5 49.9 + - + -
990M GLY* 1.3 71.4 - - - -
992M MET* 1.3 60.0 + - - +
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Residues in contact with MET 992 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578M VAL* 5.2 0.9 - - - -
670M GLN 3.6 0.7 - - - +
671M ASN* 3.4 8.1 - - - -
672M VAL* 3.0 31.3 + - - +
674M VAL* 3.7 18.6 - - + -
676M ILE* 5.9 4.7 - - + -
841M ASN* 3.5 17.3 - - - +
871M LEU* 3.9 18.4 - - + -
884M GLN* 3.2 37.5 - - + +
887M GLU* 4.0 12.6 - - - +
888M THR* 3.2 26.0 - - - +
990M GLY 3.6 0.4 + - - -
991M GLN* 1.3 75.4 - - - +
993M PHE* 1.3 68.0 + - - +
994M ILE* 3.6 28.4 + - + -
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Residues in contact with PHE 993 (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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565M GLN* 5.3 0.2 - - - -
575M GLN 3.1 22.7 - - - -
577M PRO* 3.4 34.5 - - + -
578M VAL* 5.4 0.4 - - - +
666M LEU 4.9 0.2 - - - -
668M LEU* 3.6 22.2 - - + -
669M GLY* 3.0 36.1 - - - -
670M GLN 3.7 9.9 - - - -
671M ASN* 3.9 6.5 + - - +
841M ASN* 3.3 24.6 - - - +
842M ARG* 3.2 42.1 + - + +
887M GLU* 2.7 25.0 + - - +
992M MET* 1.3 71.6 - - - +
994M ILE* 1.3 59.7 + - - +
995M MET* 4.1 13.0 - - + -
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Residues in contact with ILE 994 (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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669M GLY* 3.9 0.4 - - - -
670M GLN 3.0 21.2 + - - +
672M VAL* 3.5 25.4 - - + -
674M VAL* 5.0 0.9 - - + -
700M TYR* 2.4 35.6 + - + +
839M LEU* 4.0 21.1 - - + -
840M ALA 3.2 16.4 - - - +
841M ASN* 4.1 5.8 - - + +
869M VAL* 4.6 13.0 - - + -
871M LEU* 4.8 10.8 - - + -
992M MET* 3.6 30.5 + - + -
993M PHE* 1.3 81.0 - - - +
995M MET* 1.3 68.5 + - - +
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Residues in contact with MET 995 (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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564M MET* 4.6 4.9 - - + +
565M GLN* 4.1 33.9 - - + -
568M ALA* 3.8 16.8 - - + -
668M LEU* 3.7 16.6 - - + +
669M GLY* 3.6 26.0 - - - +
700M TYR* 3.9 3.8 - - - -
839M LEU* 3.3 7.1 - - - +
840M ALA* 2.8 59.4 + - + +
841M ASN* 3.6 25.8 - - - +
842M ARG* 4.2 2.7 - - + +
993M PHE* 4.1 10.5 - - + +
994M ILE* 1.3 75.7 - - - +
996M LYS* 1.3 61.7 + - - +
997M LEU* 3.6 8.5 + - + +
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Residues in contact with LYS 996 (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* 2.8 29.1 + - + +
571M LEU* 3.9 15.3 - - + +
668M LEU 4.8 0.4 + - - -
700M TYR* 3.5 40.0 + - + +
702M SER* 3.3 23.2 + - - +
831M ARG* 3.4 25.5 + - - +
832M LYS 3.8 6.9 + - - -
833M LEU* 4.3 10.5 - - + -
837M ASP* 3.3 27.0 + - + -
838M LYS 3.7 9.9 - - - +
839M LEU* 3.9 2.5 - - + -
995M MET* 1.3 70.2 - - - +
997M LEU* 1.3 68.1 + - - +
1000M MET* 3.6 24.5 - - + +
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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