Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 3CPA
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 ASP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LYS* 3.6 17.8 + - - -
52A PHE 3.3 8.5 - - - +
53A SER* 2.7 32.5 + - - -
54A THR 4.5 0.2 + - - -
55A GLY 4.7 0.9 - - - +
57A SER 5.5 1.2 - - - +
58A ASN* 5.4 0.7 - - - -
59A ARG* 3.6 34.2 + - - +
60A PRO 3.1 5.1 + - - -
61A ALA* 3.1 6.6 - - + -
62A ILE* 2.9 26.9 + - - +
103A MET* 1.3 78.0 - - - +
105A ILE* 1.3 66.2 + - - +
106A PHE* 3.8 19.8 - - + -
186A HIS* 5.3 1.2 - - - -
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Residues in contact with ILE 105 (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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50A LEU 3.3 3.3 - - - +
51A LYS* 3.3 2.8 - - - +
52A PHE* 2.7 43.2 + - + -
62A ILE* 3.5 23.6 - - + +
64A ILE* 4.0 21.3 - - + -
86A PHE* 3.7 27.6 - - + -
96A PHE* 3.5 39.0 - - + -
99A ILE* 4.6 5.8 - - + -
100A LEU* 4.3 13.0 - - + -
103A MET 5.2 0.4 - - - +
104A ASP* 1.3 79.2 - - - +
106A PHE* 1.3 70.7 + - - +
301A MET* 4.1 11.2 - - + -
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Residues in contact with PHE 106 (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 LEU* 4.0 5.8 - - + -
49A VAL* 3.7 21.5 - - + -
50A LEU 3.3 4.5 - - - -
51A LYS* 3.6 44.4 - - + -
61A ALA* 3.5 22.9 - - + -
62A ILE 2.9 9.3 + - - +
63A TRP* 3.6 21.5 - - + -
64A ILE* 2.9 27.7 + - - +
104A ASP* 3.8 12.8 - - + -
105A ILE* 1.3 75.9 - - - +
107A LEU* 1.3 61.8 + - - +
108A GLU 4.2 0.2 - - - -
182A PHE* 3.6 24.2 - + - -
186A HIS* 3.6 23.8 - + - -
189A PHE* 3.4 18.2 - + + -
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Residues in contact with LEU 107 (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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22A MET* 5.1 0.7 - - - +
48A TYR 4.4 0.2 - - - +
49A VAL* 3.6 4.1 - - - +
50A LEU* 2.8 42.1 + - + +
52A PHE* 3.9 18.4 - - + -
64A ILE* 3.4 25.6 - - + -
66A LEU* 3.6 26.7 - - + -
79A GLY 3.8 11.2 - - - +
82A PHE* 4.6 8.1 - - + -
83A ALA* 3.8 34.1 - - + +
86A PHE* 4.2 11.2 - - + -
105A ILE* 4.7 0.9 - - + -
106A PHE* 1.3 73.4 - - - +
108A GLU* 1.3 59.5 - - - +
109A ILE* 3.8 17.1 + - + +
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Residues in contact with GLU 108 (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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38A ILE* 4.6 2.7 - - - -
47A ILE* 3.3 24.5 - - - +
48A TYR 3.7 17.3 - - - +
49A VAL* 4.4 2.7 - - + +
63A TRP* 3.1 34.6 - - + -
64A ILE 2.7 15.3 + - - +
65A ASP* 4.1 0.9 - - + -
66A LEU* 2.8 33.5 + - - +
106A PHE 4.2 0.2 - - - -
107A LEU* 1.3 72.3 - - - +
109A ILE* 1.3 59.4 + - - +
110A VAL 4.0 2.2 - - - +
111A THR* 3.2 38.9 + - - +
179A ILE* 3.2 20.2 - - - +
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Residues in contact with ILE 109 (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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18A ILE* 4.0 16.4 - - + -
21A PHE* 4.7 2.2 - - + -
22A MET* 4.5 19.8 - - + +
48A TYR 4.5 3.6 + - - -
50A LEU* 4.1 24.7 - - + -
66A LEU* 3.2 21.2 - - - +
76A GLN* 3.3 44.8 - - + +
79A GLY* 3.9 18.2 - - - +
80A VAL* 3.9 21.3 - - + +
83A ALA* 4.6 2.2 - - + -
107A LEU* 3.8 25.0 + - + +
108A GLU* 1.3 72.7 - - - +
110A VAL* 1.3 59.7 - - - +
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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