Contacts of the strand formed by residues 76 - 82 (chain h) in PDB entry 5GJQ
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 76 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71h LYS* 4.1 0.5 - - - -
72h ILE* 3.0 11.4 + - + -
73h THR* 2.9 46.5 + - - +
74h GLU 3.7 0.2 - - - -
75h ASN* 1.3 84.8 - - + +
77h GLY* 1.3 63.0 + - - +
108h GLU* 5.6 1.8 - - + +
109h ILE* 3.5 42.2 - - + +
111h VAL* 4.0 26.9 - - + +
114h LEU* 4.0 17.0 - - + -
140h LEU* 4.0 29.6 - - + -
141h ILE 3.6 7.0 - - - +
227h PHE* 4.3 2.9 - - - -
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Residues in contact with GLY 77 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70h PHE 3.5 9.0 - - - -
76h ILE* 1.3 75.5 - - - +
78h CYS* 1.3 62.5 + - - +
140h LEU* 3.4 6.8 - - - +
141h ILE* 2.8 39.4 + - - +
227h PHE* 3.6 29.5 - - - +
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Residues in contact with CYS 78 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50h ILE* 5.6 2.9 - - - +
69h LEU* 3.5 6.7 - - - +
70h PHE* 2.9 52.2 + - - -
72h ILE* 3.9 11.0 - - + -
77h GLY* 1.3 76.8 - - - +
79h VAL* 1.3 62.0 + - - +
80h MET* 3.6 29.6 - - - -
91h VAL* 3.9 6.7 - - - -
138h MET* 4.3 4.0 - - + -
139h ILE 3.2 7.4 - - - +
140h LEU* 3.4 23.8 - - + -
141h ILE* 5.4 0.7 - - - -
227h PHE* 4.5 2.9 - - - -
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Residues in contact with VAL 79 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39h SER* 3.7 17.5 - - - +
40h VAL 6.3 0.2 - - - -
41h ALA* 5.6 0.2 - - + -
50h ILE* 3.7 21.8 - - + -
52h THR* 3.3 25.4 - - - +
68h HIS* 3.3 13.9 - - + +
69h LEU* 3.6 14.8 - - + -
78h CYS* 1.3 74.5 - - - +
80h MET* 1.3 70.0 + - - +
81h THR* 4.6 1.6 + - - +
137h CYS 3.5 3.3 - - - +
138h MET* 3.6 1.2 - - - -
139h ILE* 2.9 60.8 + - + +
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Residues in contact with MET 80 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39h SER* 4.5 1.2 + - - -
52h THR* 5.7 0.2 - - - +
68h HIS* 3.1 37.0 + - - +
70h PHE* 3.9 10.3 - - + -
78h CYS* 3.6 13.5 - - - -
79h VAL* 1.3 74.1 - - - +
81h THR* 1.3 66.9 + - - +
87h SER* 3.6 45.1 - - - +
90h GLN* 3.4 25.8 - - - +
91h VAL* 3.7 19.5 - - + -
136h CYS* 4.1 4.7 - - + -
137h CYS 3.4 6.3 - - - +
138h MET* 3.5 39.0 - - + -
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Residues in contact with THR 81 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32h ILE* 3.4 16.7 - - + +
37h LEU* 4.3 12.1 - - + +
39h SER* 3.1 28.5 + - - +
79h VAL* 4.5 3.1 + - - +
80h MET* 1.3 77.6 + - - +
82h GLY* 1.3 61.2 + - - +
87h SER* 4.4 0.9 + - - -
136h CYS* 3.3 2.3 - - - -
137h CYS* 2.8 41.6 + - - +
139h ILE* 5.8 0.5 - - - +
168h ALA* 3.9 15.8 - - + +
169h GLY* 3.7 33.9 - - - +
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Residues in contact with GLY 82 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32h ILE* 3.2 26.0 + - - -
35h GLY* 4.8 12.6 - - - -
37h LEU* 6.3 1.0 - - - +
68h HIS* 5.3 7.2 + - - -
80h MET 4.2 0.8 + - - -
81h THR* 1.3 79.6 - - - +
83h MET* 1.3 68.0 + - - -
84h THR* 3.3 5.9 + - - -
87h SER* 4.1 2.5 + - - -
135h GLY 3.4 6.5 - - - -
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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