Contacts of the strand formed by residues 60 - 68 (chain A) in PDB entry 2B4J
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 ILE 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A CYS* 4.8 9.6 - - + -
57A SER* 3.2 41.4 + - - +
58A PRO 3.5 2.6 + - - -
59A GLY* 1.3 83.6 - - - +
61A TRP* 1.3 64.7 + - - +
78A HIS* 3.9 5.4 + - - -
79A VAL* 3.2 33.8 + - + +
80A ALA 4.8 0.7 + - - -
111A LYS* 5.3 2.5 - - + -
112A THR* 3.5 26.5 - - + +
114A HIS* 3.3 37.5 - - + +
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Residues in contact with TRP 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 GLY 3.5 13.6 + - - -
60A ILE* 1.3 80.6 - - - +
62A GLN* 1.3 62.8 + - - +
63A LEU* 4.6 4.7 - - + -
76A ALA* 4.0 13.7 - - + -
77A VAL 3.2 8.7 - - - -
78A HIS* 3.5 51.2 - + + -
79A VAL* 4.3 2.2 - - - -
83A TYR* 3.8 19.7 - + - -
85A GLU* 5.1 0.9 - - + -
104A LEU* 3.9 22.9 - - + -
108A TRP* 3.6 41.5 - + + -
109A PRO* 3.3 17.9 + - + -
110A VAL* 3.7 21.2 - - + +
112A THR 2.9 9.7 + - - +
113A VAL* 3.3 13.7 - - + -
114A HIS* 2.8 29.1 + - - +
200A ILE* 3.8 6.5 - - + -
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Residues in contact with GLN 62 (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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61A TRP* 1.3 74.7 - - - +
63A LEU* 1.3 62.9 + - - +
76A ALA* 3.4 2.8 - - - -
77A VAL* 2.9 36.4 + - + +
79A VAL* 3.9 12.0 - - + +
114A HIS* 3.3 22.8 - - + +
150A VAL* 3.1 30.1 + - - +
151A ILE* 2.9 52.8 - - + +
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Residues in contact with LEU 63 (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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61A TRP* 4.6 5.2 - - + -
62A GLN* 1.3 80.2 - - - +
64A ASP* 1.3 64.6 + - - +
74A LEU* 4.5 8.5 - - + -
75A VAL 3.4 9.0 - - - +
76A ALA* 3.6 20.9 - - + -
97A THR* 4.3 6.3 - - + -
100A PHE* 4.7 7.4 - - + -
101A LEU* 3.9 30.7 - - + -
104A LEU* 4.6 7.4 - - + -
113A VAL* 4.4 20.0 - - + -
114A HIS 2.9 13.9 + - - +
115A THR* 3.7 27.7 - - + +
116A ASP 4.6 1.2 + - - -
121A PHE* 3.9 23.8 - - + -
151A ILE* 3.6 5.4 - - - +
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Residues in contact with ASP 64 (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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63A LEU* 1.3 77.1 - - - +
65A CYS* 1.3 68.1 + - - +
74A LEU* 3.5 2.8 - - - +
75A VAL* 2.7 41.0 + - - +
116A ASP* 4.6 14.0 - - - +
121A PHE* 3.7 10.1 - - - -
151A ILE* 3.3 27.8 - - + +
152A GLU* 4.9 4.2 - - - +
155A ASN* 2.7 44.8 + - - +
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Residues in contact with CYS 65 (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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64A ASP* 1.3 85.5 - - - +
66A THR* 1.3 61.2 + - - +
67A HIS* 4.8 2.8 - - + -
72A VAL* 4.1 13.5 - - + -
73A ILE 3.2 6.5 - - - +
74A LEU* 3.7 24.7 - - - -
89A ILE* 4.5 3.1 - - - -
92A GLU* 3.4 34.1 - - - +
120A ASN* 3.8 22.4 - - - -
121A PHE* 4.1 5.0 - - + -
301A PO4 3.9 9.2 + - - -
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Residues in contact with THR 66 (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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64A ASP 4.3 0.2 + - - -
65A CYS* 1.3 76.0 - - - +
67A HIS* 1.3 63.5 + - - +
72A VAL* 3.6 2.4 - - - +
73A ILE* 2.9 54.1 + - + +
75A VAL* 4.1 13.7 - - + +
155A ASN* 4.0 21.6 - - + +
158A LEU* 4.9 5.4 - - + -
159A LYS* 2.9 32.6 + - + -
301A PO4 2.6 26.5 + - - -
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Residues in contact with HIS 67 (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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65A CYS 4.8 2.9 - - - -
66A THR* 1.3 81.1 + - - +
68A LEU* 1.3 62.7 + - - +
70A GLY* 5.7 3.6 - - - +
71A LYS 3.3 11.0 - - - +
72A VAL* 3.7 25.2 - - + +
73A ILE* 4.9 0.7 - - - +
92A GLU* 2.7 36.7 + - - -
159A LYS* 2.8 25.8 + - - -
301A PO4 3.2 28.7 + - - +
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Residues in contact with LEU 68 (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 HIS* 1.3 79.7 - - - +
69A GLU* 1.3 73.7 + - + +
70A GLY 3.1 2.2 - - - -
71A LYS 2.9 21.5 + - - +
73A ILE* 4.0 13.8 - - + +
159A LYS* 4.0 26.7 - - + +
162A ILE* 3.6 46.9 - - + -
172A LEU* 3.4 21.4 - - + +
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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