Contacts of the strand formed by residues 100 - 104 (chain P) in PDB entry 3J7Y
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 VAL 100 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1506 ARG* 3.3 51.6 - - - +
81P ARG* 5.5 1.1 - - - +
92P LEU* 3.4 30.1 - - + -
93P VAL 3.6 6.1 - - - +
94P GLU* 3.8 23.8 - - + +
98P GLY 3.3 6.7 + - - +
99P LYS* 1.3 69.7 - - - +
101P VAL* 1.3 61.8 + - - +
102P VAL 3.5 12.3 - - - +
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Residues in contact with VAL 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476 HIS 5.3 0.2 - - - +
1506 ARG* 4.3 12.5 - - - +
1516 LEU* 3.3 43.0 - - + +
1546 TYR* 3.3 52.7 - - + -
1556 TYR* 5.3 2.2 - - + -
78P HIS* 4.3 13.7 - - + +
93P VAL 2.8 17.4 + - - +
95P HIS 4.8 2.2 - - - +
99P LYS 3.7 9.6 - - - +
100P VAL* 1.3 73.8 - - - +
102P VAL* 1.3 56.7 + - - +
138P ALA* 5.2 0.2 - - + -
140P ILE* 3.6 24.5 - - + -
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Residues in contact with VAL 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476 HIS* 5.7 2.5 - - - +
1506 ARG* 4.1 3.8 - - - +
1516 LEU* 4.2 4.7 - - + -
92P LEU* 3.5 0.7 - - - -
93P VAL* 2.8 37.4 + - + -
100P VAL* 3.5 4.0 - - - +
101P VAL* 1.3 84.0 - - + +
103P SER* 1.3 67.9 + - - +
131P LEU* 3.8 19.5 - - + -
134P ARG* 3.5 36.3 - - + +
135P CYS* 4.3 1.6 - - - +
138P ALA* 3.8 19.3 - - + -
140P ILE* 3.6 23.3 - - + -
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Residues in contact with SER 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476 HIS* 3.4 20.4 + - - -
1506 ARG* 2.7 30.6 + - - +
90P GLU* 6.0 2.2 - - - -
91P ALA 3.2 13.9 - - - -
92P LEU* 3.7 15.9 - - - +
102P VAL* 1.3 84.9 - - - +
104P ALA* 1.3 63.7 + - - +
105P SER* 6.3 0.4 - - - -
108P GLU* 5.4 1.0 - - - +
131P LEU* 4.7 2.5 - - - -
134P ARG* 2.9 25.3 + - - +
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Residues in contact with ALA 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476 HIS* 5.4 0.2 - - - -
90P GLU* 5.8 0.2 - - - -
91P ALA 2.8 37.6 + - - -
103P SER* 1.3 79.2 - - - +
105P SER* 1.3 59.0 + - - +
108P GLU* 5.6 1.3 - - - -
111P ILE* 6.1 0.9 - - + -
127P ILE* 3.2 37.5 - - + +
130P VAL* 4.2 4.0 - - + -
131P LEU* 4.1 17.0 - - + +
134P ARG* 3.4 17.0 - - - +
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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