Contacts of the strand formed by residues 84 - 89 (chain M) in PDB entry 2GLJ
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 GLY 84 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M THR* 4.1 4.6 + - - -
78M ALA 4.6 0.2 - - - -
79M ASN* 3.7 8.1 - - - +
80M ASN* 2.9 42.0 + - - +
82M GLY 3.4 0.6 - - - -
83M LYS* 1.3 80.8 - - - +
85M LEU* 1.3 63.3 + - - +
291M LEU 3.5 9.4 - - - -
292M VAL* 4.8 6.7 - - - -
293M ASP 5.6 0.2 - - - -
303M THR* 4.4 3.3 - - - +
306M GLN* 6.3 0.4 - - - -
308M LYS* 5.0 0.9 - - - -
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Residues in contact with LEU 85 (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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46M THR* 4.2 11.2 + - - +
49M ILE* 3.4 34.8 - - + -
50M LYS* 3.3 31.2 - - - +
77M TYR* 3.9 17.5 - - + -
78M ALA 3.6 12.6 - - - +
84M GLY* 1.3 75.2 - - - +
86M ILE* 1.3 77.2 + - - +
87M MET* 4.3 12.8 - - + -
106M ILE* 5.9 0.7 - - + -
289M THR 4.0 0.5 - - - +
290M ILE* 3.7 1.3 - - - +
291M LEU* 2.8 57.3 + - + +
292M VAL* 5.7 1.0 - - - +
308M LYS* 5.2 1.5 - - - +
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Residues in contact with ILE 86 (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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76M VAL 4.2 0.2 - - - +
77M TYR* 3.3 3.5 - - - -
78M ALA* 2.9 53.2 + - + +
85M LEU* 1.3 79.2 - - - +
87M MET* 1.3 67.5 + - - +
88M PHE* 3.6 31.2 - - + -
288M ILE* 4.9 3.1 - - + -
289M THR 3.1 11.2 - - - +
290M ILE* 4.3 13.9 - - + -
308M LYS* 3.7 16.6 - - + -
309M PHE* 3.6 40.4 - - + +
312M ASN* 4.5 5.4 - - - +
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Residues in contact with MET 87 (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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49M ILE* 5.4 0.2 - - + -
53M GLU* 3.1 43.7 - - - +
57M TYR* 4.1 14.4 - - + -
76M VAL 3.5 2.9 - - - -
77M TYR* 4.3 7.6 - - + -
85M LEU* 4.3 22.7 - - + -
86M ILE* 1.3 75.5 - - - +
88M PHE* 1.3 64.2 + - - +
274M PHE* 3.3 24.5 - - + -
277M MET* 3.7 19.5 - - + -
288M ILE* 3.1 9.2 - - - +
289M THR* 2.7 59.4 + - + +
291M LEU* 5.5 0.9 - - + -
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Residues in contact with PHE 88 (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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57M TYR* 3.1 25.5 - - - -
59M ASN* 5.9 1.1 - - - -
75M LYS* 3.5 6.6 - - - -
76M VAL* 2.8 35.8 + - + +
77M TYR* 5.3 1.1 - - - -
78M ALA* 5.3 1.8 - - + -
86M ILE* 3.6 34.3 - - + -
87M MET* 1.3 78.8 - - - +
89M LEU* 1.3 62.3 + - - +
90M ILE* 4.8 6.7 - - + -
95M LEU* 6.1 0.7 - - + -
99M PHE* 4.6 6.1 - + - -
277M MET* 3.9 1.3 - - - -
286M THR* 5.0 5.2 - - + -
287M CYS 3.8 1.3 - - - -
288M ILE* 3.1 30.3 - - + -
312M ASN* 3.5 27.1 - - - -
313M THR* 4.1 26.0 - - + -
316M ASP* 4.0 24.9 - - + +
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 4.8 5.2 - - - +
73M GLY* 4.8 6.3 - - - +
74M ASP 3.4 14.4 - - - +
75M LYS* 4.5 18.8 - - + -
88M PHE* 1.3 79.0 - - - +
90M ILE* 1.3 68.9 + - - +
277M MET* 4.1 11.0 - - + +
280M MET* 3.2 36.3 - - + +
281M LYS* 5.4 0.7 - - - -
282M ASN 6.1 0.7 - - - +
283M ALA* 4.0 18.6 - - + +
286M THR* 3.1 15.2 - - - +
287M CYS* 3.2 42.2 + - - +
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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