Contacts of the helix formed by residues 80 - 98 (chain A) in PDB entry 2JI8
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 SER 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE 3.8 8.9 + - - -
35A PRO* 4.2 5.0 - - - +
79A VAL* 1.3 77.0 - - - +
81A ALA* 1.3 70.5 + - - +
82A PRO* 2.9 6.2 - - - +
83A GLY 2.8 16.8 + - - -
84A PHE* 4.0 2.0 - - - -
106A GLY 3.2 17.6 + - - -
107A SER* 4.1 8.4 - - - -
108A SER* 4.1 7.1 + - - -
120A TYR* 4.4 4.2 - - - -
121A GLU* 2.7 30.8 + - - +
125A GLN* 3.3 13.2 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 1.3 71.1 - - - +
82A PRO* 1.3 69.6 - - + +
84A PHE* 3.5 2.0 + - - +
85A LEU* 2.9 34.8 + - - +
121A GLU 3.6 15.7 - - - +
123A MET* 4.0 19.6 - - + +
125A GLN* 3.1 12.0 + - - -
425B TRP* 3.6 33.9 - - + +
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.9 0.2 - - + -
80A SER 3.3 5.2 - - - +
81A ALA* 1.3 94.0 - - + +
83A GLY* 1.3 59.8 + - - +
85A LEU* 3.6 7.7 + - + +
86A ASN* 3.3 28.4 + - - +
121A GLU* 3.2 33.7 - - + +
61B TYR* 5.8 1.3 - - - +
425B TRP* 3.6 25.5 - - + +
427B VAL* 4.1 22.4 - - + -
1563B TPP 3.9 22.7 - - + +
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Residues in contact with GLY 83 (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 GLU* 3.7 24.5 - - - +
78A THR* 3.6 8.1 + - - -
79A VAL* 3.6 19.6 - - - +
80A SER 2.8 11.1 + - - -
82A PRO* 1.3 73.3 - - - +
84A PHE* 1.3 64.9 + - - -
86A ASN* 3.1 6.2 + - - +
87A GLY 3.0 18.0 + - - -
1563B TPP 3.9 2.1 - - - +
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Residues in contact with PHE 84 (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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78A THR* 3.2 12.6 - - - +
79A VAL 3.0 19.5 + - - +
80A SER 3.3 1.3 + - - +
81A ALA 3.7 4.9 - - - +
83A GLY* 1.3 71.3 - - - +
85A LEU* 1.3 69.8 + - + +
87A GLY* 3.0 4.0 + - - -
88A VAL* 2.8 60.5 + - + -
103A LEU* 4.2 3.5 - - + +
105A SER* 3.8 3.8 - - - +
123A MET* 3.6 33.0 - - - -
125A GLN* 3.3 40.4 - - + +
128A VAL* 3.8 11.9 - - + -
129A ALA* 4.0 7.9 - - + -
165A TYR* 3.6 40.4 - + - -
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Residues in contact with LEU 85 (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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81A ALA 2.9 19.1 + - - +
82A PRO* 3.7 7.2 - - + +
84A PHE* 1.3 77.8 - - + +
86A ASN* 1.3 62.3 + - - +
88A VAL* 3.4 16.9 - - + +
89A THR* 3.2 21.5 - - - +
123A MET* 3.9 23.8 - - + -
128A VAL* 4.3 8.1 - - + -
88B VAL* 6.2 1.6 - - + -
89B THR* 3.9 30.1 - - + +
92B ALA* 3.9 26.9 - - + -
132B HIS* 3.9 20.6 - - + +
425B TRP* 3.9 15.9 - - + -
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Residues in contact with ASN 86 (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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55A HIS* 3.2 32.5 + - + +
56A GLU* 2.9 25.4 + - + +
57A GLN* 3.6 12.0 - - - +
82A PRO 3.3 15.3 + - - +
83A GLY 3.1 7.0 + - - +
85A LEU* 1.3 77.6 - - - +
87A GLY* 1.3 58.6 + - - +
89A THR* 2.5 29.5 + - - -
57B GLN* 2.7 28.5 + - - +
61B TYR* 4.9 2.5 + - - -
89B THR* 4.4 4.9 - - - +
428B MET 5.1 0.8 + - - -
457B PHE* 4.7 1.0 - - - -
1563B TPP 3.4 13.9 - - - +
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Residues in contact with GLY 87 (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 GLU* 4.0 18.9 - - - +
76A CYS* 5.0 2.7 - - - -
78A THR* 4.6 0.9 - - - -
83A GLY 3.0 9.3 + - - -
84A PHE 3.0 7.1 + - - -
86A ASN* 1.3 75.3 - - - +
88A VAL* 1.3 57.7 + - - +
90A SER* 2.9 22.5 + - - -
91A LEU 3.0 10.2 + - - -
101A MET* 4.5 2.8 - - - +
103A LEU* 3.7 21.3 - - - +
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Residues in contact with VAL 88 (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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84A PHE* 2.8 47.6 + - + +
85A LEU* 3.4 27.6 - - + +
86A ASN 3.4 0.2 - - - -
87A GLY* 1.3 69.8 - - - +
89A THR* 1.3 70.3 + - + +
91A LEU* 4.0 10.3 - - + -
92A ALA* 3.0 24.6 + - - +
103A LEU* 3.5 11.3 - - + +
128A VAL* 5.3 2.0 - - + -
129A ALA* 4.0 20.4 - - + -
132A HIS* 4.2 22.0 - - + +
85B LEU* 6.0 2.2 - - + -
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Residues in contact with THR 89 (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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57A GLN* 3.0 28.4 + - - +
61A TYR* 4.7 5.1 + - - -
85A LEU 3.2 16.6 - - - +
86A ASN* 2.5 24.0 + - - +
88A VAL* 1.3 79.6 - - + +
90A SER* 1.3 59.8 + - - +
92A ALA* 3.4 5.0 - - - +
93A HIS* 3.4 17.3 + - - +
425A TRP* 4.8 1.0 - - - -
85B LEU* 3.9 35.8 - - + +
86B ASN* 4.6 2.5 - - - +
89B THR* 3.7 22.9 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.6 39.5 + - - +
60A GLY* 3.5 29.2 - - - -
61A TYR* 3.6 15.1 + - - -
64A SER* 4.8 0.3 - - - -
87A GLY 2.9 8.5 + - - -
89A THR* 1.3 76.0 + - - +
91A LEU* 1.3 55.1 + - - +
92A ALA 3.2 0.9 - - - -
93A HIS* 2.9 8.8 + - - +
94A ALA* 2.7 32.4 + - - +
101A MET* 4.4 2.8 - - - +
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Residues in contact with LEU 91 (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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87A GLY 3.0 11.4 + - - +
88A VAL* 3.6 19.3 - - + +
90A SER* 1.3 74.5 - - - +
92A ALA* 1.3 57.2 + - - +
94A ALA* 3.0 3.1 + - - +
95A THR* 2.8 32.7 + - - -
101A MET* 3.8 30.7 - - + +
103A LEU* 4.0 24.0 - - + -
132A HIS 3.7 7.4 - - - +
133A CYS* 3.9 21.8 - - + -
163A GLY* 3.4 28.5 - - - -
164A VAL 3.7 9.6 - - - +
165A TYR* 4.0 19.1 - - + +
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Residues in contact with ALA 92 (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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88A VAL 3.0 17.9 + - - +
89A THR 3.4 7.4 - - - +
91A LEU* 1.3 75.9 - - - +
93A HIS* 1.3 53.5 + - - +
95A THR* 3.5 2.6 + - - -
96A THR* 2.7 37.7 + - - -
132A HIS* 3.4 32.0 + - + +
425A TRP* 3.9 9.8 - - + -
85B LEU* 3.7 21.1 - - + -
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Residues in contact with HIS 93 (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 TYR* 3.7 26.7 - + + +
64A SER* 3.6 19.4 + - - -
89A THR 3.4 5.0 + - - +
90A SER 2.9 10.3 + - - +
92A ALA* 1.3 76.5 - - - +
94A ALA* 1.3 68.3 + - - +
96A THR* 3.4 1.6 + - - -
97A ASN* 3.0 52.7 + - - +
99A PHE* 4.2 4.9 - + - -
422A SER 4.1 15.5 - - - -
423A GLY* 5.4 0.4 - - - -
425A TRP* 3.9 16.1 - - + -
427A VAL* 3.7 17.9 - - + +
430A ILE* 3.9 13.1 - - + +
434A TYR* 2.8 27.7 + - - -
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Residues in contact with ALA 94 (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 SER* 4.0 6.3 - - - -
90A SER 2.7 9.7 + - - +
91A LEU* 3.0 8.9 + - - +
93A HIS* 1.3 77.1 - - - +
95A THR* 1.3 64.4 + - - +
97A ASN* 3.0 4.2 + - - +
98A CYS 2.9 19.8 + - - -
99A PHE* 3.0 33.9 + - + +
101A MET* 3.6 33.9 - - + -
163A GLY 4.4 3.4 - - - +
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Residues in contact with THR 95 (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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91A LEU 2.8 13.2 + - - -
92A ALA 3.7 3.6 - - - -
94A ALA* 1.3 71.9 - - - +
96A THR* 1.3 64.1 + - - +
98A CYS* 3.3 15.9 + - - -
131A PRO 5.9 0.7 - - - +
132A HIS 2.7 29.9 + - - +
133A CYS* 3.4 21.5 - - - -
134A LYS* 4.3 10.3 - - + +
160A ARG* 5.4 2.9 - - - -
161A PRO 4.7 1.9 - - - +
162A GLY* 4.3 2.9 - - - -
163A GLY* 3.2 22.2 + - - +
282A ARG* 5.6 0.5 + - - -
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Residues in contact with THR 96 (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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92A ALA 2.7 22.2 + - - -
93A HIS 3.7 4.5 - - - -
94A ALA 3.3 0.2 - - - -
95A THR* 1.3 78.1 - - - +
97A ASN* 1.3 61.5 + - - +
98A CYS 3.7 0.2 + - - -
282A ARG* 2.8 30.6 + - - +
424A THR* 3.7 23.8 + - + -
425A TRP* 3.3 46.5 - - + +
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Residues in contact with ASN 97 (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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93A HIS* 3.0 47.9 + - - +
94A ALA 3.0 2.0 + - - -
96A THR* 1.3 81.5 - - - +
98A CYS* 1.3 70.9 + - - +
99A PHE* 3.5 32.2 - - + -
222A LYS* 2.9 44.7 + - - +
282A ARG* 4.4 0.7 - - - -
423A GLY* 3.6 4.4 - - - -
424A THR* 2.9 25.2 + - - +
425A TRP* 4.6 4.4 - - - +
1568A ADP 4.0 1.9 + - - +
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Residues in contact with CYS 98 (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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94A ALA 2.9 3.5 + - - -
95A THR 3.3 5.8 + - - -
96A THR 4.3 0.9 - - - -
97A ASN* 1.3 83.3 - - - +
99A PHE* 1.3 64.1 + - - +
100A PRO* 3.9 2.1 - - - +
160A ARG* 3.6 37.5 - - + -
161A PRO* 3.2 41.2 - - + +
226A TYR* 4.8 6.1 - - - -
282A ARG* 3.9 16.4 - - - -
1568A ADP 3.8 27.9 - - + -
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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