Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 5C7G
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 PHE 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 3.7 25.4 - - - +
56A VAL 3.4 4.9 - - - +
57A ASP* 3.4 37.7 - - + -
90A VAL* 3.2 10.6 - - - +
91A SER* 2.9 39.9 + - - +
93A ASN 3.9 4.3 - - - -
94A GLY* 3.4 34.5 - - - -
97A TRP* 3.6 23.8 - + + -
129A THR* 3.8 1.0 + - - -
130A ARG* 1.3 102.4 - - + +
132A VAL* 1.3 61.6 + - - +
133A ARG 4.2 0.4 - - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE 4.1 0.2 - - - +
55A GLN* 3.1 3.2 - - - -
56A VAL* 2.9 42.5 + - + +
58A LEU* 4.3 18.4 - - + -
64A VAL* 4.3 21.5 - - + -
67A VAL* 4.3 21.3 - - + -
88A ILE* 3.9 21.5 - - + -
89A ASP 3.8 1.8 - - - -
90A VAL* 4.5 3.8 - - + -
123A PHE* 4.8 3.1 - - + -
129A THR* 4.4 8.7 - - + -
131A PHE* 1.3 77.0 - - - +
133A ARG* 1.3 63.4 + - - +
134A ILE* 4.1 7.0 + - + +
147A PHE* 5.5 1.3 - - + -
149A VAL* 4.3 9.4 - - + -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.6 67.0 - - + +
54A ILE 3.5 5.4 - - - +
55A GLN* 2.9 29.7 + - + +
88A ILE* 3.2 7.1 - - - -
89A ASP* 2.8 47.6 + - + +
97A TRP* 3.3 44.5 - - + +
132A VAL* 1.3 73.1 - - - +
134A ILE* 1.3 62.4 + - - +
135A LYS* 3.9 13.8 + - + +
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.3 6.8 - - - +
54A ILE* 2.8 38.8 + - + +
67A VAL* 3.9 20.2 - - + -
69A THR* 4.8 3.6 - - + -
86A TYR* 3.8 23.8 - - + -
87A LYS 3.6 2.9 - - - -
88A ILE* 4.5 12.8 - - + -
132A VAL* 4.9 7.9 - - + +
133A ARG* 1.3 73.1 - - - +
135A LYS* 1.3 60.8 + - - +
136A PRO* 3.4 3.6 - - + +
145A MET* 3.7 28.5 - - + -
147A PHE* 3.8 47.3 - - + -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR 4.9 7.9 - - - +
52A GLU 4.0 7.6 - - - +
53A TRP* 4.2 13.5 - - + -
86A TYR* 3.9 2.0 - - - -
87A LYS* 2.8 56.5 + - + +
89A ASP* 2.9 41.7 + - - +
99A THR* 4.2 6.9 + - - +
133A ARG* 4.0 17.7 - - + +
134A ILE* 1.3 77.8 - - - +
136A PRO* 1.3 70.2 - - - +
137A ALA* 4.3 1.4 - - - +
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Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 4.4 5.4 - - + -
49A SER 5.2 0.4 - - - +
50A TYR* 3.7 24.9 - - - +
52A GLU 3.5 17.3 - - - +
53A TRP* 4.3 2.0 - - - -
83A VAL* 4.0 13.7 - - + -
85A THR 4.0 1.1 - - - +
86A TYR* 3.9 9.4 - - + -
134A ILE* 3.4 13.0 - - + +
135A LYS* 1.3 84.2 - - - +
137A ALA* 1.3 59.8 + - - +
139A TRP* 4.0 3.4 - - + -
143A ILE* 3.9 42.4 - - + -
145A MET* 4.0 17.5 - - - -
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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