Contacts of the strand formed by residues 81 - 90 (chain T) in PDB entry 1V2J
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 GLN 81 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65T VAL 3.5 0.9 - - - +
66T ARG* 3.6 1.0 - - - -
67T LEU* 3.0 46.5 + - + +
79T ASN 4.5 4.4 + - - +
80T GLU* 1.3 80.4 - - - +
82T PHE* 1.3 62.5 + - - +
83T ILE* 4.3 8.4 - - + +
112T ALA* 3.6 12.1 - - - +
113T SER* 2.8 55.7 + - - -
115T ASN* 3.9 8.1 - - - +
118T VAL* 3.7 20.8 - - - +
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Residues in contact with PHE 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T GLN* 3.9 31.0 - - - +
65T VAL 3.5 3.4 - - - -
66T ARG* 3.6 54.1 - - + -
70T GLU* 3.8 13.2 - - - -
76T VAL* 5.1 17.0 - - + -
80T GLU* 3.8 21.5 - - + -
81T GLN* 1.3 78.6 - - - +
83T ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T GLN* 4.3 3.5 - - - +
65T VAL* 2.7 44.4 + - - +
67T LEU* 4.2 8.5 - - + -
81T GLN* 4.3 10.1 - - + +
82T PHE* 1.3 83.1 - - - +
84T SER* 1.3 71.2 + - - +
108T LEU* 3.8 20.4 - - + +
109T LYS* 4.6 1.6 - - + -
110T SER* 3.6 35.7 - - - +
111T ALA 4.4 2.7 - - - +
112T ALA* 3.7 37.2 - - + -
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Residues in contact with SER 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T ILE 3.8 9.4 + - - -
64T GLN* 4.2 14.4 + - - +
83T ILE* 1.3 79.9 - - - +
85T ALA* 1.3 61.4 + - - +
108T LEU* 3.8 1.6 - - - -
109T LYS* 3.0 51.7 + - - +
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Residues in contact with ALA 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T ILE* 3.0 35.9 + - + +
65T VAL* 4.8 1.5 - - + +
83T ILE 3.8 1.0 + - - -
84T SER* 1.3 76.4 - - - +
86T SER* 1.3 60.4 + - - +
87T LYS* 4.4 3.4 - - - +
88T SER* 4.5 7.0 - - - +
106T ILE* 3.6 28.0 - - + -
107T LYS 3.6 5.6 - - - +
108T LEU* 4.6 2.5 - - - +
109T LYS* 4.2 5.9 + - - -
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Residues in contact with SER 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T SER 3.7 2.4 + - - -
85T ALA* 1.3 74.3 - - - +
87T LYS* 1.3 68.7 + - - +
107T LYS* 2.8 36.3 + - - +
108T LEU 3.9 1.9 + - - -
109T LYS* 3.8 34.7 - - - +
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Residues in contact with LYS 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ALA* 3.4 2.7 - - - -
86T SER* 1.3 86.6 + - - +
88T SER* 1.3 63.8 + - - +
89T ILE* 4.0 22.1 - - + +
105T LEU 3.9 0.5 - - - +
106T ILE* 3.5 4.1 - - - +
107T LYS* 2.9 58.5 + - + +
245T ASN* 3.0 31.6 + - + +
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Residues in contact with SER 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T TYR* 3.8 35.6 - - - -
60T LYS 4.5 2.4 + - - -
63T ILE* 4.3 13.7 - - - +
85T ALA* 4.5 5.4 - - - +
87T LYS* 1.3 76.1 + - - +
89T ILE* 1.3 62.8 + - - +
90T VAL* 3.8 2.8 + - - +
104T MET* 4.2 10.3 - - - -
105T LEU 3.4 4.5 - - - -
106T ILE* 4.0 14.4 - - - +
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Residues in contact with ILE 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T TRP* 4.1 14.8 - - + -
87T LYS* 4.0 20.6 - - + -
88T SER* 1.3 74.8 - - - +
90T VAL* 1.3 67.9 + - - +
91T HIS 3.8 0.5 + - - -
92T PRO* 5.8 1.6 - - + -
104T MET* 3.4 3.3 - - - -
105T LEU* 2.6 40.9 + - + +
237T TRP* 3.9 13.3 - - + -
241T THR* 3.8 22.0 - - + -
245T ASN* 3.5 35.9 - - - +
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Residues in contact with VAL 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T ALA* 3.6 22.4 - - + +
59T TYR* 3.8 42.6 - - + -
88T SER 3.8 2.2 + - - +
89T ILE* 1.3 80.1 - - - +
91T HIS* 1.3 77.3 + - - +
92T PRO* 3.2 9.2 - - - +
94T TYR* 3.8 14.8 - - + -
103T ILE 4.1 3.6 - - - -
104T MET* 4.1 10.5 - - + -
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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