Contacts of the strand formed by residues 53 - 61 (chain A) in PDB entry 7C17
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A MET 3.1 7.7 + - - -
52A PRO* 1.3 74.4 - - - +
54A CYS* 1.3 64.8 + - - -
55A ALA 4.2 0.4 - - - -
147A GLN 3.8 0.2 - - - +
148A ARG* 3.4 9.8 - - - -
149A GLY 3.1 27.6 + - - +
177A TYR* 3.4 16.7 + - - -
179A PRO* 4.5 12.3 - - - -
210A THR* 5.8 2.9 - - - -
211A ILE* 6.5 0.4 - - - -
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Residues in contact with CYS 54 (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 GLY* 1.3 72.8 - - - -
55A ALA* 1.3 61.5 + - - +
88A LEU 5.0 4.3 - - - +
89A ALA* 5.4 0.9 - - - -
90A VAL* 3.7 29.7 + - + +
92A VAL* 3.7 31.0 - - - -
96A ASP 5.7 0.9 - - - -
146A VAL* 3.7 17.5 - - + -
147A GLN 3.7 3.4 - - - -
148A ARG* 3.4 35.4 - - - -
176A CYS 5.0 1.8 - - - +
177A TYR* 4.4 1.0 + - - -
179A PRO* 5.7 1.3 - - - +
210A THR* 4.7 11.7 + - - +
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Residues in contact with ALA 55 (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 CYS* 1.3 72.8 - - - +
56A VAL* 1.3 65.6 + - - +
57A THR* 3.8 2.6 + - - +
86A LYS 5.7 2.0 - - - +
88A LEU 5.8 2.7 - - - -
90A VAL* 5.9 1.3 - - - -
146A VAL* 3.5 8.9 - - - +
147A GLN 3.4 28.9 + - - +
175A ALA* 4.1 2.5 - - - -
176A CYS* 3.4 48.5 - - - +
177A TYR* 3.7 15.8 - - + -
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Residues in contact with VAL 56 (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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55A ALA* 1.3 76.5 - - - +
57A THR* 1.3 62.7 + - - +
58A GLU 4.6 0.2 - - - +
59A VAL* 3.7 30.1 - - + -
85A LEU* 3.3 43.8 + - + +
86A LYS* 4.5 5.8 - - - +
88A LEU* 5.2 5.2 - - + +
90A VAL* 6.1 2.7 - - + -
144A ILE* 3.7 23.8 - - + -
145A LYS 4.4 2.2 - - - -
146A VAL* 5.0 4.0 - - + -
173A VAL* 3.5 34.0 - - + +
174A ASP 4.0 1.6 - - - +
175A ALA* 3.9 10.7 - - - -
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Residues in contact with THR 57 (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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55A ALA 4.3 3.6 - - - +
56A VAL* 1.3 78.0 - - - +
58A GLU* 1.3 68.0 + - - +
145A LYS* 2.6 34.2 + - - +
147A GLN* 3.7 16.5 + - + +
158A ARG* 3.2 27.7 + - - +
172A LEU* 3.5 1.6 - - - -
173A VAL* 2.6 33.4 + - - -
175A ALA* 3.8 13.7 - - + -
177A TYR* 3.4 26.2 - - + +
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Residues in contact with GLU 58 (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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57A THR* 1.3 89.7 + - - +
59A VAL* 1.3 63.7 + - - +
60A GLU 4.3 0.2 - - - -
143A ARG* 4.0 1.6 - - - +
144A ILE* 3.8 0.3 - - - -
145A LYS* 2.8 69.4 + - + +
158A ARG* 3.9 14.9 + - - +
162A GLU* 4.6 12.0 - - - +
166A ARG* 4.8 9.9 - - - -
170A ARG* 3.4 29.4 + - + +
171A LEU 3.4 3.4 - - - -
172A LEU* 3.8 20.1 - - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A VAL* 3.7 24.9 - - + -
57A THR 4.3 0.2 - - - -
58A GLU* 1.3 78.3 - - - +
60A GLU* 1.3 60.8 + - - +
61A ILE* 3.7 25.1 - - + -
82A LEU* 3.8 22.9 - - + -
85A LEU* 3.8 18.6 - - + -
142A MET* 4.0 10.8 - - + -
143A ARG 3.3 15.0 - - - +
144A ILE* 4.0 6.3 - - + -
170A ARG* 4.3 1.3 - - - -
171A LEU* 2.9 39.1 + - + +
173A VAL* 4.4 1.8 - - + -
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Residues in contact with GLU 60 (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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59A VAL* 1.3 71.2 - - - +
61A ILE* 1.3 76.8 + - - +
62A ASP* 3.9 6.2 + - - +
64A VAL 4.8 2.9 - - - +
142A MET* 3.6 3.6 - - - -
143A ARG* 2.7 63.6 + - + +
167A PRO* 6.6 0.2 - - + -
168A ILE 4.1 6.7 - - - +
169A GLY* 3.4 31.3 - - - +
170A ARG* 3.4 28.5 - - - +
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Residues in contact with ILE 61 (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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59A VAL* 3.7 16.5 + - + -
60A GLU* 1.3 83.6 - - - +
62A ASP* 1.3 71.4 + - - +
64A VAL* 3.4 28.9 - - + +
71A LYS* 4.0 5.2 - - + +
78A ILE* 4.0 40.8 - - + +
81A ILE* 5.1 10.5 - - + -
82A LEU* 5.3 2.7 - - + -
140A ILE* 4.0 21.1 - - + -
141A SER 3.4 16.4 - - - +
142A MET* 3.7 21.3 - - + -
169A GLY* 4.4 3.0 + - - +
171A LEU* 4.5 7.6 - - + +
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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