Contacts of the strand formed by residues 105 - 114 (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 LEU 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.3 6.6 - - - +
83A ASN* 2.8 46.2 + - - +
103A GLY 3.5 1.6 + - - -
104A ASP* 1.3 71.2 - - - +
106A VAL* 1.3 61.9 + - - +
107A LYS* 3.9 11.4 - - + +
124A THR* 3.6 19.1 - - + -
125A PHE 3.5 5.2 - - - +
126A VAL* 4.5 3.4 - - + +
139A LYS* 4.3 12.3 - - + +
142A VAL* 4.1 8.3 - - + -
143A ILE* 3.8 29.2 - - + -
315A PHE* 3.9 31.4 - - + -
316A VAL 3.1 25.8 - - - +
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Residues in contact with VAL 106 (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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39A SER* 5.1 2.0 - - - +
80A ILE* 3.6 28.9 - - + -
81A SER 4.2 2.2 - - - -
82A VAL* 4.3 4.7 - - + +
100A LEU* 3.8 19.1 - - + -
104A ASP* 4.0 3.4 - - + +
105A LEU* 1.3 79.2 - - - +
107A LYS* 1.3 65.0 + - - +
108A ILE* 3.9 6.7 - - + -
123A HIS 3.7 1.0 - - - +
124A THR* 3.2 5.2 - - - -
125A PHE* 2.8 62.1 + - + +
127A VAL* 3.4 32.5 - - + -
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Residues in contact with LYS 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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79A SER 3.5 1.7 - - - +
80A ILE* 3.2 5.7 - - - +
81A SER* 2.9 52.5 + - - +
83A ASN 3.2 11.9 + - - +
85A CYS 2.7 30.6 + - - -
86A VAL 3.3 19.3 - - - +
105A LEU* 3.9 5.6 - - + +
106A VAL* 1.3 74.7 - - - +
108A ILE* 1.3 61.6 + - - +
109A ASP* 4.1 0.6 - - + +
123A HIS 3.3 5.6 - - - +
124A THR* 3.5 17.5 - - - +
316A VAL* 2.8 37.1 + - + +
317A ALA 3.9 0.4 - - - -
318A GLN* 3.6 35.0 - - + +
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Residues in contact with ILE 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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32A LEU* 3.7 23.0 - - + +
35A LEU* 3.8 50.5 - - + -
36A VAL* 4.1 4.9 - - + +
39A SER* 4.2 5.2 - - - +
48A LEU* 5.7 0.2 - - + -
78A THR* 4.4 3.4 - - + -
79A SER 3.5 6.3 - - - +
80A ILE* 4.1 16.8 - - + -
106A VAL* 3.9 14.8 - - + -
107A LYS* 1.3 77.1 - - - +
109A ASP* 1.3 62.0 + - - +
110A LEU* 4.3 7.6 - - + -
122A ALA* 3.1 4.8 - - - +
123A HIS 2.9 32.2 + - - +
125A PHE* 3.7 24.2 - - + -
318A GLN* 5.0 0.2 - - - -
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Residues in contact with ASP 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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76A PHE* 4.2 18.5 - - - +
77A PRO 3.6 2.6 - - - +
78A THR* 3.5 1.4 - - - +
79A SER* 2.9 42.4 + - - +
87A CYS* 5.5 3.8 - - - +
88A HIS* 5.0 8.2 + - - +
107A LYS 5.3 0.9 - - - +
108A ILE* 1.3 75.9 - - - +
110A LEU* 1.3 67.5 + - - +
120A ASN* 5.7 0.2 - - - +
121A VAL 3.4 10.6 - - - +
122A ALA* 3.8 10.1 - - + -
318A GLN* 3.6 16.9 + - - +
320A LYS* 2.9 32.5 + - - +
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Residues in contact with LEU 110 (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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28A ALA* 3.9 24.0 - - + +
31A VAL* 3.9 15.3 - - + -
32A LEU* 4.1 13.5 - - + +
35A LEU* 3.9 28.3 - - + -
56A ILE* 4.3 15.3 - - + -
76A PHE* 3.6 18.4 - - - +
77A PRO 4.5 0.4 - - - -
78A THR* 4.1 14.6 - - - +
108A ILE* 4.3 8.7 - - + -
109A ASP* 1.3 77.6 + - - +
111A GLY* 1.3 61.3 + - - +
112A VAL* 4.4 1.1 - - + -
120A ASN* 3.6 2.1 - - - +
121A VAL* 3.0 52.2 + - + +
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Residues in contact with GLY 111 (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* 4.0 4.9 - - - +
74A ILE* 3.7 5.0 - - - -
75A ALA* 2.8 21.0 + - - -
76A PHE* 3.0 20.6 + - - +
110A LEU* 1.3 76.1 - - - +
112A VAL* 1.3 65.5 - - - +
119A ALA 3.3 5.2 - - - -
120A ASN* 3.3 21.3 - - - -
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Residues in contact with VAL 112 (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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24A GLY* 3.7 29.4 - - - +
27A ILE* 4.0 9.9 - - + -
28A ALA* 3.8 29.6 - - + +
56A ILE* 3.9 21.8 - - + -
60A THR* 3.7 27.6 - - + -
73A GLY 3.4 5.4 - - - +
75A ALA* 3.6 3.6 - - - +
110A LEU* 4.4 0.9 - - + -
111A GLY* 1.3 80.3 - - - +
113A HIS* 1.3 65.2 + - - +
117A PHE 3.9 0.2 - - - +
118A ILE* 3.5 3.3 - - - -
119A ALA* 2.8 32.8 + - - +
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Residues in contact with HIS 113 (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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24A GLY* 5.7 0.2 - - - -
60A THR* 4.1 0.5 - - - +
71A LYS* 3.7 15.0 - - + -
72A LYS* 3.4 28.5 - - - +
73A GLY* 2.9 45.2 + - - +
74A ILE 3.6 24.2 + - - -
75A ALA* 4.0 8.7 - - + -
112A VAL* 1.3 76.2 - - - +
114A VAL* 1.3 69.0 + - - +
116A GLY* 3.0 24.2 + - - -
117A PHE 3.2 16.8 - - - +
118A ILE* 4.1 0.4 - - + -
276A MET* 3.8 29.9 - - + +
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Residues in contact with VAL 114 (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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20A LYS* 3.8 21.4 - - + +
23A MET* 4.6 0.4 - - + -
24A GLY* 3.8 28.5 - - - +
60A THR* 4.8 4.5 - - + -
63A ILE* 3.8 19.1 - - + -
64A PHE* 3.7 35.9 - - + -
70A MET* 4.3 7.2 - - - -
72A LYS* 4.1 8.1 - - + -
112A VAL* 4.7 3.8 - - + -
113A HIS* 1.3 78.3 - - - +
115A ASP* 1.3 70.4 + - - +
117A PHE* 3.0 25.9 + - - +
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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