Contacts of the strand formed by residues 61 - 79 (chain J) in PDB entry 6MZL
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 VAL 61 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J TYR* 3.7 34.1 - - + +
56J VAL 3.4 1.2 - - - +
57J ARG* 3.2 3.0 - - - -
58J VAL 2.9 36.7 + - - +
59J ASP* 3.7 11.0 - - + +
60J ARG* 1.3 77.7 - - - +
62J PRO* 1.3 75.8 - - + +
63J LEU* 3.7 4.5 + - + +
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Residues in contact with PRO 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ILE* 3.8 22.9 - - + -
56J VAL 3.7 3.6 - - - +
57J ARG* 4.1 10.5 - - + +
60J ARG 3.4 10.3 - - - +
61J VAL* 1.3 89.2 - - + +
63J LEU* 1.3 68.0 + - - +
99J VAL 5.3 2.6 - - - +
103J LEU* 4.0 29.2 - - + +
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Residues in contact with LEU 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 4.5 6.7 - - + -
21J PRO* 3.7 16.4 - - + -
24J TYR* 3.7 56.3 - - + +
55J ILE* 3.5 3.1 - - - -
56J VAL 2.8 39.4 + - - +
58J VAL* 4.5 4.9 - - + -
61J VAL* 4.4 5.4 - - + +
62J PRO* 1.3 81.7 - - - +
64J ALA* 1.3 64.9 + - - +
65J SER* 3.3 1.9 + - - -
97J SER* 3.9 14.8 - - - -
98J THR 3.5 15.3 - - - +
99J VAL* 3.8 19.3 - - + +
103J LEU* 4.2 2.9 - - - -
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J GLY 3.9 5.2 - - - +
63J LEU* 1.3 70.1 - - - +
65J SER* 1.3 58.9 + - - +
96J VAL 3.7 1.2 - - - +
97J SER* 3.5 0.3 - - - -
98J THR* 2.8 37.4 + - - +
99J VAL 5.4 0.6 - - - -
100J ASP 3.9 14.1 - - - +
101J GLY* 3.9 18.4 - - - +
102J ASP 3.8 22.0 - - - +
103J LEU* 3.8 14.4 - - + +
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Residues in contact with SER 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J HIS* 3.5 9.2 - - - +
54J GLY 2.9 41.2 + - - +
56J VAL* 3.3 12.7 - - - +
63J LEU 3.3 7.4 + - - -
64J ALA* 1.3 72.7 - - - +
66J LYS* 1.3 61.8 + - - +
95J LEU* 3.7 22.9 - - - -
96J VAL 3.0 7.6 - - - -
97J SER* 2.6 26.6 + - - -
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Residues in contact with LYS 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ARG 3.6 2.9 - - - -
53J HIS* 4.3 17.4 + - + +
65J SER* 1.3 76.4 - - - +
67J LEU* 1.3 62.0 + - - +
68J VAL* 3.5 15.6 + - + +
94J MET 3.3 4.0 - - - +
95J LEU* 3.8 2.9 - - - -
96J VAL* 2.9 37.2 + - + +
129J LYS* 4.0 25.8 - - - +
130J PHE* 3.6 36.6 - - + -
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Residues in contact with LEU 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 4.1 25.4 - - + -
16J PHE* 4.9 6.3 - - + -
47J LEU* 5.9 4.9 - - + -
51J GLY 3.4 21.1 - - - +
52J ARG* 2.7 35.2 + - - +
66J LYS* 1.3 70.0 - - - +
68J VAL* 1.3 60.1 + - - +
93J GLN* 3.4 45.1 - - + +
94J MET 3.6 15.5 - - - +
95J LEU* 3.9 17.6 - - + +
130J PHE* 3.5 22.9 - - - +
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J LYS* 4.0 28.0 - - + +
67J LEU* 1.3 78.3 - - - +
69J ASP* 1.3 62.8 + - - +
70J LEU* 5.1 0.4 - - + -
93J GLN* 3.3 6.6 - - - +
94J MET* 2.9 54.8 + - + +
96J VAL* 4.2 14.4 - - + -
129J LYS 4.5 1.8 - - - +
130J PHE* 3.3 19.3 - - - +
131J ILE 5.3 0.2 - - - -
132J TRP* 3.8 35.7 - - + +
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Residues in contact with ASP 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ARG* 3.3 29.6 + - - -
68J VAL* 1.3 71.8 - - - +
70J LEU* 1.3 66.6 + - - +
92J CYS* 3.5 7.0 - - - +
93J GLN* 3.3 28.7 + - - +
130J PHE* 3.0 15.4 + - - +
131J ILE* 5.1 6.7 - - + +
132J TRP* 3.2 25.8 + - - +
144J ARG* 3.8 9.1 + - - +
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Residues in contact with LEU 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 4.5 5.9 + - - -
17J ILE* 4.3 17.9 - - + -
68J VAL* 3.8 0.6 + - + -
69J ASP* 1.3 75.6 - - - +
71J PRO* 1.3 70.7 - - + +
72J CYS 3.4 12.4 - - - +
74J MET* 4.4 11.9 - - + -
91J ILE* 4.7 3.4 - - + +
92J CYS* 2.5 41.1 + - - +
93J GLN 4.1 11.4 - - - +
94J MET* 3.9 19.7 - - + -
132J TRP* 3.7 27.6 - - + -
134J HIS 4.6 1.3 - - - +
136J ILE* 3.8 28.7 - - + -
144J ARG* 4.2 2.1 + - - -
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Residues in contact with PRO 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 3.1 21.7 + - - -
686A GLU* 4.6 2.8 - - - +
69J ASP 3.7 0.2 - - - -
70J LEU* 1.3 87.0 - - + +
72J CYS* 1.3 60.0 + - + +
132J TRP* 3.4 19.5 - - + +
133J ASN 4.1 0.2 - - - -
134J HIS 3.4 28.9 - - - +
135J GLY* 5.0 0.4 - - - -
143J VAL* 3.7 16.6 - - + -
144J ARG* 3.4 33.0 - - + +
148J PHE* 3.7 25.7 - - + -
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Residues in contact with CYS 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 4.0 2.9 - - - +
682A GLU* 3.8 28.4 - - + +
683A TYR 3.5 22.0 - - - +
684A SER* 4.6 3.4 - - - -
685A GLU 5.4 1.3 - - - -
686A GLU* 5.5 0.2 - - - +
70J LEU* 4.1 15.6 - - - +
71J PRO* 1.3 82.6 - - + +
73J VAL* 1.3 64.9 + - - +
74J MET* 3.5 6.6 + - - +
91J ILE 4.2 3.5 - - - +
92J CYS* 4.7 1.2 - - - -
135J GLY* 5.2 0.7 - - - -
140J LEU* 4.5 7.9 - - - -
143J VAL* 4.1 20.4 - - - -
148J PHE* 3.6 27.1 - - - -
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Residues in contact with VAL 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A HIS* 3.3 29.8 - - + +
617A ARG* 3.3 23.8 - - - +
682A GLU* 4.0 0.3 - - - -
683A TYR* 3.1 36.6 + - + +
685A GLU 3.8 12.3 + - - +
686A GLU 3.7 18.6 - - - +
687A ASN* 5.7 0.2 - - - -
688A GLY 5.8 0.2 - - - +
691A MET* 3.9 30.1 - - + -
72J CYS* 1.3 73.3 - - - +
74J MET* 1.3 62.5 + - - +
75J GLU* 5.1 1.3 - - + -
90J ASP* 4.4 8.3 - - - +
91J ILE 4.3 2.0 - - - -
92J CYS* 5.4 0.2 - - - -
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Residues in contact with MET 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 3.7 28.3 - - + -
681A ALA 3.4 15.3 - - - +
682A GLU* 3.5 38.6 - - + +
757A MET* 5.4 0.4 - - - -
779A ILE* 4.1 13.7 - - + -
17J ILE* 4.6 15.9 - - - -
70J LEU* 4.4 10.8 - - + -
72J CYS 3.5 4.0 + - - +
73J VAL* 1.3 76.7 - - - +
75J GLU* 1.3 60.7 + - - +
90J ASP* 3.4 8.0 - - - +
91J ILE* 2.8 48.1 + - + +
136J ILE* 3.7 23.1 - - + -
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Residues in contact with GLU 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A LEU* 3.4 4.0 - - - -
681A ALA* 2.5 46.8 + - + +
683A TYR* 2.6 46.6 + - + +
691A MET* 3.5 11.7 - - + +
692A MET* 3.6 16.2 + - - +
73J VAL* 5.1 0.7 - - + -
74J MET* 1.3 74.3 - - - +
76J SER* 1.3 57.4 + - - +
77J LEU* 3.4 17.4 - - + +
87J LYS* 2.9 35.1 + - + +
89J ALA 3.4 5.2 - - - +
90J ASP* 3.3 17.5 - - - +
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Residues in contact with SER 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A LEU* 5.1 2.9 - - - -
679A ILE 3.5 9.2 - - - -
680A LEU* 3.7 21.3 - - - -
763A LEU* 5.0 4.5 - - - -
15J GLN* 2.7 28.1 + - - -
75J GLU* 1.3 72.1 - - - +
77J LEU* 1.3 53.4 + - - +
87J LYS* 3.7 1.6 - - - +
88J THR* 2.5 52.8 + - - -
89J ALA* 2.9 19.3 + - - +
91J ILE* 4.0 5.2 - - - +
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Residues in contact with LEU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A LEU* 3.2 7.3 - - - +
679A ILE* 2.9 48.1 + - + +
681A ALA* 3.8 14.8 - - + -
692A MET* 4.5 9.2 - - + -
698A THR* 3.8 19.7 - - + -
743A PHE* 4.7 6.1 - - + -
75J GLU* 3.4 37.7 - - + +
76J SER* 1.3 73.9 - - - +
78J LYS* 1.3 59.8 + - - +
85J PHE* 3.7 30.7 - - + -
86J TYR 3.3 6.7 - - - +
87J LYS* 3.7 18.6 - - + +
88J THR* 3.9 1.3 - - - +
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Residues in contact with LYS 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A ARG* 3.7 15.4 - - - +
665A MET* 4.1 17.5 - - - -
670A ASP 2.4 33.5 + - - +
671A LEU* 4.1 4.9 - - - +
672A THR 3.2 15.5 + - - +
675A ASP* 3.1 31.1 + - - -
676A GLY* 5.0 2.7 - - - -
677A ASP 3.4 5.2 - - - +
678A LEU* 3.7 15.9 - - + -
77J LEU* 1.3 73.9 - - - +
79J THR* 1.3 64.4 + - - +
80J ILE* 5.3 3.4 - - - -
85J PHE* 3.4 3.7 - - - +
86J TYR* 2.6 54.9 + - + +
88J THR* 3.6 16.2 - - + +
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Residues in contact with THR 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A GLY* 4.1 1.0 - - - -
677A ASP* 2.6 57.0 + - + +
678A LEU* 5.2 1.8 - - - -
679A ILE* 5.6 0.9 - - + -
719A TYR* 4.7 4.7 - - + -
78J LYS* 1.3 80.9 - - - +
80J ILE* 1.3 77.3 + - - +
81J ASP 3.6 0.3 + - - -
82J LYS* 3.0 34.4 + - + +
84J THR 3.3 15.7 + - - -
85J PHE* 3.4 26.0 - - + -
86J TYR* 5.4 2.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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