Contacts of the strand formed by residues 73 - 79 (chain A) in PDB entry 3C5H
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL 4.1 1.2 - - - +
71A ASP* 3.2 26.2 - - + +
72A HIS* 1.3 79.3 - - - +
74A LEU* 1.3 66.7 + - - +
94A VAL* 3.4 38.4 - - + -
95A GLU 3.0 14.8 - - - +
96A GLN* 3.4 24.2 - - - +
97A THR* 4.5 1.3 - - - +
99A PHE* 4.4 1.1 - - - -
125A LEU* 4.0 30.5 - - + -
126A ALA 5.0 2.5 - - - -
127A SER* 3.7 23.3 - - - -
130A LYS* 2.9 42.6 + - + -
150A MET* 4.1 7.2 - - - -
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Residues in contact with LEU 74 (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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36A SER* 4.5 3.4 - - - +
67A VAL 4.6 7.0 - - - +
68A VAL* 4.3 13.9 - - + -
73A PHE* 1.3 79.0 - - - +
75A TYR* 1.3 59.4 + - - +
76A TRP* 3.7 14.2 + - + +
94A VAL* 3.2 10.3 - - - +
95A GLU* 2.9 52.3 + - + +
97A THR* 4.9 0.9 - - + -
99A PHE* 3.6 35.9 - - + -
130A LYS* 4.0 2.9 - - - +
133A TYR* 3.9 53.2 - - + -
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Residues in contact with TYR 75 (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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67A VAL 5.2 0.2 + - - -
74A LEU* 1.3 70.0 - - - +
76A TRP* 1.3 59.4 + - - +
77A GLY* 3.4 32.5 - - - -
92A HIS* 2.7 40.5 + - + -
93A ILE 3.5 11.2 - - - -
94A VAL* 4.0 9.2 - - + -
130A LYS* 3.6 25.7 - - + +
131A LEU 4.4 4.6 + - - +
132A MET* 3.3 22.9 - - + -
133A TYR* 2.8 30.0 + - - +
148A LYS* 2.8 30.9 + - - -
149A GLN 4.0 1.1 - - - -
150A MET* 3.5 42.2 - - + -
151A PRO* 3.8 4.5 - - + -
155A LEU* 4.4 0.7 - - + -
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Residues in contact with TRP 76 (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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36A SER* 3.4 36.6 - - - -
39A CYS* 3.5 22.0 - - + +
40A ASN* 3.4 29.8 - - + -
43A VAL* 3.3 21.7 - - + +
44A ARG* 3.2 53.2 + - - -
54A HIS* 3.5 14.1 - + - -
74A LEU* 4.0 10.0 - - + +
75A TYR* 1.3 73.4 - - - +
77A GLY* 1.3 57.0 + - - +
93A ILE* 2.8 18.1 + - + +
95A GLU* 2.9 41.0 + - + +
132A MET* 3.5 3.3 - - - +
133A TYR* 3.4 41.1 - + - -
134A PHE 4.2 2.7 - - - -
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Residues in contact with GLY 77 (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 VAL* 4.5 4.9 - - - -
75A TYR* 3.4 25.2 - - - -
76A TRP* 1.3 79.6 - - - +
78A GLU* 1.3 60.2 + - - -
91A MET 3.7 0.7 - - - +
92A HIS* 3.5 2.6 - - - -
93A ILE* 3.0 28.1 + - - +
132A MET* 3.5 18.4 - - - -
148A LYS* 4.8 0.2 - - - -
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Residues in contact with GLU 78 (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 VAL* 4.4 8.5 - - - +
75A TYR* 3.7 2.9 + - - +
77A GLY* 1.3 73.9 - - - -
79A VAL* 1.3 71.9 + - - +
80A SER* 4.1 17.1 + - - -
90A LYS* 4.4 13.9 - - + +
91A MET 3.2 7.0 - - - +
92A HIS* 3.6 32.6 - - + +
132A MET* 4.7 1.8 - - - -
148A LYS* 3.8 19.9 + - - +
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Residues in contact with VAL 79 (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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42A PHE* 3.4 41.5 - - + +
43A VAL* 3.8 28.7 - - + +
78A GLU* 1.3 76.9 - - - +
80A SER* 1.3 67.8 + - - +
90A LYS* 3.5 4.7 - - - -
91A MET* 2.8 57.3 + - + +
93A ILE* 4.7 2.7 - - + -
308A UNX 4.0 14.6 - - - -
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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