Contacts of the strand formed by residues 113 - 117 (chain P) in PDB entry 3EXG
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 113 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76P PRO 3.2 12.8 + - - +
77P ILE* 3.5 14.6 - - + +
78P CYS* 2.7 31.2 + - - +
112P ILE* 1.3 81.8 - - - +
114P PHE* 1.3 69.3 + - - +
115P ARG* 4.7 0.4 - - + -
157P ILE* 4.3 12.8 - - + -
160P ALA* 3.4 48.2 - - + +
161P ILE* 3.7 8.5 - - + +
167P VAL* 3.4 11.2 - - + +
169P VAL* 4.2 8.1 - - + -
1012P K 3.8 6.5 - - - -
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Residues in contact with PHE 114 (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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63P ALA* 4.7 7.0 - - + -
67P VAL* 4.0 15.0 - - + -
78P CYS* 3.3 24.5 - - + -
80P PHE* 3.6 32.5 - + + -
83P PHE* 4.1 9.9 - - + -
93P VAL* 3.6 42.2 - - + -
97P ALA* 4.6 2.9 - - + -
112P ILE* 3.5 46.2 - - + -
113P VAL* 1.3 73.1 - - - +
115P ARG* 1.3 57.7 + - - +
166P PRO* 4.8 3.4 - - + -
167P VAL 3.0 11.5 + - - +
168P VAL* 3.5 14.2 - - + -
169P VAL* 2.7 33.0 + - - +
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Residues in contact with ARG 115 (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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9P ILE* 4.4 2.6 - - - +
13P MET* 4.1 21.9 - - - +
25P LEU* 4.5 4.0 - - - +
39P VAL* 3.5 25.4 - - - +
77P ILE* 4.0 19.5 - - + -
78P CYS 3.1 11.0 + - - +
79P GLU* 2.6 47.4 + - - +
80P PHE* 3.1 24.1 + - - +
83P PHE* 3.8 8.7 - - - -
113P VAL* 4.7 1.3 - - + -
114P PHE* 1.3 77.3 - - - +
116P GLY* 1.3 63.0 + - - +
117P PRO* 5.2 0.6 - - - +
157P ILE* 4.1 19.3 - - + -
169P VAL* 3.3 24.9 - - + +
171P GLU* 2.6 41.3 + - - +
176P TYR* 3.8 4.9 + - - -
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Residues in contact with GLY 116 (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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79P GLU* 4.5 1.6 - - - -
80P PHE 3.8 7.9 - - - -
83P PHE* 3.0 17.7 - - - -
115P ARG* 1.3 83.6 - - - +
117P PRO* 1.3 77.8 - - - +
169P VAL 3.6 0.4 + - - -
171P GLU* 3.3 30.4 + - - -
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Residues in contact with PRO 117 (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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37P TYR* 4.1 18.6 - - + -
79P GLU* 5.8 1.6 - - + -
80P PHE 4.1 0.4 - - - +
81P MET 3.0 26.5 - - - +
82P THR* 3.5 15.9 - - + -
83P PHE 3.0 25.5 + - - -
115P ARG* 5.2 0.9 - - - +
116P GLY* 1.3 82.1 - - - +
118P ASN* 1.3 58.8 + - - +
171P GLU 3.4 10.5 - - - +
173P GLU* 3.8 30.5 - - + +
176P TYR* 3.4 18.7 - - + +
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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