Contacts of the strand formed by residues 75 - 79 (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 ARG 75 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ASP* 3.2 27.6 + - - -
22P LYS* 2.9 23.8 + - + +
23P VAL* 3.5 34.9 - - + +
24P PHE 3.6 1.6 + - - +
73P GLY 4.3 6.1 + - - +
74P LEU* 1.3 80.7 - - - +
76P PRO* 1.3 67.5 - - - +
77P ILE* 3.7 2.1 + - - +
111P PRO* 3.9 20.5 - - + +
161P ILE* 3.4 16.8 + - + +
162P ARG* 3.1 26.3 + - - +
163P ASP 3.4 11.5 + - - -
164P ASN* 3.3 30.3 + - - +
1012P K 4.4 0.2 - - - -
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Residues in contact with PRO 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P PHE* 3.5 36.5 - - + +
26P LEU* 4.5 1.1 - - + -
66P ALA* 3.3 36.6 - - + +
70P ALA* 3.8 16.2 - - + +
74P LEU* 3.5 8.5 - - + +
75P ARG* 1.3 93.9 - - - +
77P ILE* 1.3 61.1 + - - +
78P CYS 4.0 0.7 - - - -
111P PRO 3.9 3.0 - - - +
112P ILE* 3.9 14.8 - - + -
113P VAL* 3.2 22.2 + - - +
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Residues in contact with ILE 77 (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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13P MET* 4.6 15.3 - - + -
17P LEU* 5.2 4.0 - - + -
23P VAL* 3.6 20.2 - - + -
24P PHE 2.9 16.5 + - - +
25P LEU* 3.4 22.5 - - + +
26P LEU* 3.0 27.4 + - - +
75P ARG 4.1 4.5 - - - +
76P PRO* 1.3 76.7 - - - +
78P CYS* 1.3 60.9 + - - +
113P VAL* 3.5 15.5 - - + +
115P ARG* 4.0 28.7 - - + -
157P ILE* 5.3 0.7 - - + -
161P ILE* 3.5 37.9 - - + -
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Residues in contact with CYS 78 (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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26P LEU* 3.5 6.7 - - + -
62P PHE* 3.5 36.1 - - - -
63P ALA* 4.1 5.4 - - - -
66P ALA* 3.8 26.7 - - + -
76P PRO 4.0 0.6 - - - -
77P ILE* 1.3 73.6 - - - +
79P GLU* 1.3 57.3 + - - +
80P PHE* 4.1 7.7 + - - -
112P ILE* 4.6 1.8 - - + -
113P VAL 2.7 11.6 + - - +
114P PHE* 3.3 30.6 - - + +
115P ARG* 3.1 25.6 + - - +
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Residues in contact with GLU 79 (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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25P LEU* 4.4 4.9 - - + +
26P LEU 3.0 13.1 + - - +
27P GLY* 3.6 16.3 - - - -
28P GLU 4.0 12.1 + - - +
30P VAL* 3.9 27.9 - - + +
35P GLY* 5.5 0.7 - - - -
36P ALA* 4.6 13.4 + - - +
37P TYR* 5.7 3.1 + - - -
39P VAL* 5.1 3.3 - - - +
40P SER* 4.3 10.0 + - - -
62P PHE* 3.8 11.0 - - - -
77P ILE 3.9 0.2 + - - -
78P CYS* 1.3 73.6 - - - +
80P PHE* 1.3 78.0 + - - +
81P MET* 4.0 6.3 + - - +
115P ARG* 2.6 51.6 + - - +
116P GLY* 4.5 1.3 - - - -
117P PRO* 5.8 0.2 - - + -
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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