Contacts of the strand formed by residues 72 - 82 (chain A) in PDB entry 3J2I
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 LYS 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A MET* 4.3 9.5 - - - +
60A THR* 3.0 34.8 + - + +
61A GLY* 3.7 14.5 + - - -
63A ILE* 2.5 34.1 + - + +
64A PHE 3.9 10.2 + - - -
65A LYS* 4.5 2.4 - - - +
67A GLU 5.6 1.1 - - - -
70A MET* 4.0 26.9 - - - +
71A LYS* 1.3 79.0 - - - +
73A GLY* 1.3 59.4 + - - +
113A HIS* 3.4 24.7 - - - +
114A VAL* 4.1 10.3 - - + -
115A ASP 4.3 0.4 - - - +
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Residues in contact with GLY 73 (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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56A ILE* 3.5 10.1 - - - +
57A MET* 3.8 12.1 - - - -
60A THR* 3.5 18.8 + - - +
72A LYS* 1.3 75.8 - - - +
74A ILE* 1.3 60.9 + - - -
112A VAL* 3.4 7.1 - - - +
113A HIS* 2.9 36.6 + - - +
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Residues in contact with ILE 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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53A ASP* 3.6 40.6 - - + +
56A ILE* 3.7 22.7 - - + -
57A MET* 3.8 18.8 - - + -
73A GLY* 1.3 70.5 - - - -
75A ALA* 1.3 61.4 + - - +
76A PHE* 3.6 29.2 - - - +
77A PRO* 3.6 12.8 - - + -
111A GLY 3.7 4.5 - - - +
113A HIS* 3.6 11.5 + - - -
273A PHE* 6.1 1.0 - - - -
276A MET* 3.9 12.3 - - - +
277A PRO 4.5 6.0 - - - +
278A PHE* 5.8 0.9 - - - -
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Residues in contact with ALA 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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73A GLY 3.6 2.0 + - - -
74A ILE* 1.3 74.2 - - - +
76A PHE* 1.3 59.0 + - - +
111A GLY* 2.8 12.2 + - - -
112A VAL 3.6 25.1 - - - +
113A HIS* 3.9 8.3 - - + +
118A ILE* 3.7 22.0 - - + -
120A ASN* 4.3 0.4 - - - +
195A ILE* 3.3 6.5 - - + +
276A MET* 3.9 15.0 - - - -
277A PRO* 3.2 31.1 - - - +
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Residues in contact with PHE 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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56A ILE* 4.8 1.0 - - - +
74A ILE* 3.6 4.8 - - - +
75A ALA* 1.3 77.7 - - - +
77A PRO* 1.3 86.4 - - + +
78A THR 3.5 1.9 + - - -
79A SER* 3.6 20.2 - - - -
88A HIS* 3.5 31.0 - + - -
109A ASP* 4.2 24.7 - - - +
110A LEU* 3.6 2.9 - - - +
111A GLY* 3.0 38.5 + - - +
120A ASN* 4.2 8.7 - - - +
195A ILE* 4.4 6.7 - - + -
246A ILE* 4.0 15.9 - - + -
277A PRO* 3.7 24.2 - - + -
305A PHE* 3.8 26.2 - + - -
320A LYS* 5.5 5.8 - - - +
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Residues in contact with PRO 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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53A ASP* 3.8 6.5 - - - +
74A ILE* 3.6 13.8 - - + -
76A PHE* 1.3 103.5 - - + +
78A THR* 1.3 69.2 + - - +
79A SER* 3.0 13.9 + - - -
90A SER* 4.7 0.2 - - - +
109A ASP 3.6 0.9 - - - +
246A ILE* 3.8 31.2 - - + -
277A PRO* 3.7 22.0 - - + +
278A PHE* 3.8 11.4 - - - -
279A THR* 4.0 24.7 - - + +
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Residues in contact with THR 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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35A LEU* 3.7 25.6 - - + -
48A LEU 4.2 1.1 - - - +
49A CYS* 3.5 40.0 - - - +
52A GLY* 3.5 6.4 - - - -
53A ASP* 2.8 38.4 + - - +
56A ILE* 4.2 2.6 - - - +
76A PHE 3.5 1.8 + - - -
77A PRO* 1.3 71.3 - - - +
79A SER* 1.3 60.1 + - - +
80A ILE* 4.2 13.0 - - + -
90A SER* 3.5 13.9 + - - -
108A ILE* 4.4 6.1 - - + -
109A ASP 3.5 6.1 - - - +
110A LEU* 4.1 12.1 - - + +
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Residues in contact with SER 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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49A CYS* 4.5 0.2 - - - -
76A PHE* 3.6 5.9 - - - -
77A PRO 3.0 14.5 + - - -
78A THR* 1.3 72.9 + - - +
80A ILE* 1.3 65.9 + - - +
81A SER* 4.1 2.0 - - - -
88A HIS* 4.1 18.4 - - - -
89A PHE 3.3 11.7 - - - -
90A SER* 4.1 0.3 - - - -
107A LYS 3.5 1.4 - - - +
108A ILE* 3.5 1.0 - - - +
109A ASP* 2.9 44.7 + - - +
246A ILE* 3.1 24.6 - - - +
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Residues in contact with ILE 80 (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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35A LEU* 5.2 0.9 - - + -
45A VAL* 3.8 26.8 - - + +
48A LEU* 3.3 41.7 - - + -
49A CYS* 4.1 17.4 - - - +
78A THR* 4.2 10.8 - - + -
79A SER* 1.3 78.0 - - - +
81A SER* 1.3 59.8 + - - +
82A VAL* 4.1 7.5 + - + +
89A PHE* 2.9 35.4 + - - -
100A LEU* 5.1 2.0 - - + -
106A VAL* 3.6 30.1 - - + -
107A LYS 3.2 2.2 - - - +
108A ILE* 4.1 18.6 - - + -
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Residues in contact with SER 81 (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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79A SER* 4.6 1.2 - - - -
80A ILE* 1.3 72.7 + - - +
82A VAL* 1.3 60.9 + - - +
85A CYS* 3.7 26.5 - - - -
86A VAL 4.0 3.8 - - - -
87A CYS* 3.3 34.0 - - - -
88A HIS 3.4 1.0 + - - -
89A PHE* 3.3 13.7 + - - +
107A LYS* 2.9 51.0 + - - -
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Residues in contact with VAL 82 (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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45A VAL* 4.6 1.6 - - + -
80A ILE* 4.1 15.7 + - + +
81A SER* 1.3 76.1 - - - +
83A ASN* 1.3 90.2 + - - +
84A ASN* 3.1 2.6 + - - +
85A CYS* 3.0 22.1 + - - +
89A PHE* 6.3 0.2 - - + -
98A TYR* 3.8 31.9 - - + +
100A LEU* 4.0 23.3 - - + -
104A ASP* 3.8 10.8 - - + -
105A LEU 3.3 10.5 - - - +
106A VAL* 4.3 8.3 - - + -
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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