Contacts of the strand formed by residues 84 - 98 (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 THR 84 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A ILE* 5.8 1.8 - - + -
590A GLN 5.2 4.0 - - - +
697A ALA* 4.3 19.7 - - + -
698A THR 3.4 10.8 - - - +
699A LYS* 2.8 36.3 + - + +
79J THR* 3.3 17.5 + - - -
80J ILE 4.7 0.9 + - - -
81J ASP* 3.3 19.1 + - - +
83J LYS* 1.3 77.0 - - - +
85J PHE* 1.3 62.8 + - - +
86J TYR* 4.3 24.5 + - + +
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Residues in contact with PHE 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 3.6 45.1 - - + -
696A MET 3.9 0.3 - - - +
697A ALA* 3.3 5.2 - - - +
698A THR* 2.6 43.5 + - + +
700A ILE* 3.5 28.7 - - + -
719A TYR* 3.5 26.5 - + - -
743A PHE* 4.6 4.3 - + - -
780A PHE* 4.7 0.4 - + - -
77J LEU* 3.7 19.1 - - + -
78J LYS 3.4 6.5 - - - +
79J THR* 3.4 19.1 - - - -
82J LYS* 3.5 26.2 - - - -
83J LYS* 4.0 7.0 - - - -
84J THR* 1.3 79.1 - - - +
86J TYR* 1.3 64.6 + - - +
87J LYS 4.2 0.2 - - - -
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Residues in contact with TYR 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLN* 3.3 22.6 + - - +
591A HIS 4.1 0.7 - - - -
592A SER* 3.9 13.5 - - - -
663A PHE* 3.2 24.8 - + - -
665A MET* 3.6 31.4 - - + -
671A LEU* 4.4 12.8 - - + -
695A GLY 4.2 9.4 - - - -
696A MET 3.5 6.5 - - - +
697A ALA* 3.6 15.7 - - + -
77J LEU* 4.1 2.0 - - - -
78J LYS* 2.6 59.0 + - + +
79J THR* 5.4 2.5 - - - -
80J ILE* 6.0 5.4 - - + -
84J THR* 4.3 25.6 - - + +
85J PHE* 1.3 73.2 - - - +
87J LYS* 1.3 61.7 + - - +
88J THR 3.4 0.3 + - - -
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Residues in contact with LYS 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A HIS* 3.2 13.5 + - - -
671A LEU* 5.0 3.8 - - - +
692A MET* 2.4 40.2 + - + +
693A GLN 3.3 27.3 - - - +
694A VAL* 3.9 7.4 - - - +
695A GLY* 3.0 26.2 + - - -
696A MET 3.2 11.6 + - - +
75J GLU* 2.9 33.1 + - + +
76J SER 4.1 5.8 - - - +
77J LEU* 3.7 21.2 - - + +
85J PHE 4.2 0.6 - - - -
86J TYR* 1.3 71.4 - - - +
88J THR* 1.3 61.9 + - - +
89J ALA 4.1 10.3 - - - +
90J ASP* 3.0 29.5 + - - -
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Residues in contact with THR 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A LEU 3.7 25.7 - - - +
672A THR 4.3 4.5 - - - +
673A GLY* 4.5 10.8 - - - +
678A LEU* 4.5 4.4 - - + +
694A VAL* 3.3 23.6 - - - +
13J GLU* 5.3 9.2 + - - +
15J GLN* 4.2 5.9 + - - -
76J SER* 2.5 42.9 + - - -
77J LEU 4.2 0.6 - - - -
78J LYS* 3.6 37.9 - - + +
86J TYR 3.7 3.8 - - - +
87J LYS* 1.3 74.6 - - - +
89J ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 89 (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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694A VAL* 4.3 7.0 - - - -
13J GLU* 4.2 15.9 - - + +
15J GLN* 3.5 31.2 - - + +
75J GLU* 3.4 6.2 - - - +
76J SER* 2.9 36.7 + - - +
87J LYS* 3.9 5.9 - - - +
88J THR* 1.3 83.7 + - - +
90J ASP* 1.3 64.7 + - - +
91J ILE* 4.9 0.4 - - + -
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Residues in contact with ASP 90 (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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616A HIS* 2.4 57.2 + - - +
618A PRO* 3.8 27.8 - - + +
694A VAL* 4.9 6.7 - - + +
13J GLU 5.5 0.9 - - - +
15J GLN 3.9 8.7 + - - +
73J VAL* 4.4 1.6 - - - +
74J MET 3.4 2.8 - - - +
75J GLU* 3.3 14.0 - - - +
87J LYS* 3.0 24.5 + - - -
89J ALA* 1.3 75.0 - - - +
91J ILE* 1.3 63.7 - - - +
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Residues in contact with ILE 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A HIS 5.5 0.7 - - - -
680A LEU* 3.7 26.5 - - + -
763A LEU* 3.7 27.8 - - + -
15J GLN* 3.5 30.5 - - + +
16J PHE* 3.8 15.3 - - - -
17J ILE* 3.7 29.4 - - + -
70J LEU* 4.7 4.6 - - + +
72J CYS 4.2 0.7 - - - +
73J VAL* 4.1 0.7 - - - +
74J MET* 2.8 47.3 + - + +
76J SER* 4.0 4.7 - - - +
90J ASP* 1.3 76.3 - - - +
92J CYS* 1.3 63.4 + - - +
93J GLN 4.0 4.5 - - - +
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Residues in contact with CYS 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A HIS 5.0 0.4 - - - +
617A ARG* 3.7 57.9 - - + +
618A PRO* 3.8 15.3 - - - -
619A PRO* 5.3 0.2 - - - -
15J GLN 4.9 0.8 + - - -
69J ASP* 3.4 4.6 - - + +
70J LEU* 2.5 47.1 + - - +
72J CYS 4.7 2.9 - - - +
73J VAL* 5.4 0.2 - - - -
90J ASP 4.4 0.4 + - - -
91J ILE* 1.3 74.4 - - - +
93J GLN* 1.3 69.3 + - - +
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Residues in contact with GLN 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A PRO 4.7 1.6 - - - +
619A PRO* 3.7 15.8 - - - +
620A LEU* 3.3 41.6 - - - +
15J GLN 5.4 0.4 + - - -
16J PHE* 3.3 15.6 - - + +
17J ILE* 2.9 24.4 + - - +
52J ARG* 4.6 5.9 - - - +
67J LEU* 3.4 26.1 - - + +
68J VAL 3.3 6.5 - - - +
69J ASP* 3.3 27.4 + - - +
70J LEU* 4.1 3.7 - - - +
91J ILE* 3.9 3.0 - - - +
92J CYS* 1.3 92.6 - - - +
94J MET* 1.3 63.0 + - - +
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Residues in contact with MET 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ILE* 3.0 30.5 - - + +
19J ARG* 3.6 50.5 - - + +
66J LYS 3.3 2.6 - - - +
67J LEU* 3.6 4.4 - - - -
68J VAL* 2.9 38.0 + - + +
70J LEU* 3.9 22.0 - - + +
93J GLN* 1.3 76.0 - - - +
95J LEU* 1.3 59.9 + - - +
96J VAL* 3.7 21.1 - - + -
132J TRP* 3.9 21.5 - - + +
136J ILE* 3.7 15.0 - - + -
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Residues in contact with LEU 95 (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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16J PHE* 4.0 20.8 - - + -
17J ILE 2.8 8.1 + - - +
18J LEU* 3.4 26.4 - - + +
19J ARG 2.9 28.1 + - - +
45J ILE* 3.9 21.1 - - + -
46J GLU 6.1 0.2 - - - +
47J LEU* 4.5 17.7 - - + -
52J ARG 5.1 0.9 - - - +
54J GLY* 5.1 2.5 - - - +
56J VAL* 3.8 17.0 - - + -
65J SER* 3.7 25.6 - - - +
66J LYS 3.4 16.6 - - - +
67J LEU* 3.9 16.9 - - + +
94J MET* 1.3 70.7 - - - +
96J VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 96 (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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19J ARG* 3.6 22.0 - - + +
64J ALA 3.7 1.4 - - - +
65J SER* 3.0 3.4 - - - -
66J LYS* 2.9 39.9 + - + +
68J VAL* 4.2 11.0 - - + -
94J MET* 3.7 38.8 - - + +
95J LEU* 1.3 73.9 - - - +
97J SER* 1.3 71.3 + - - +
98J THR* 4.1 12.5 + - + +
132J TRP* 5.3 9.4 - - + -
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Residues in contact with SER 97 (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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18J LEU* 4.5 2.3 - - - +
19J ARG 2.9 17.0 + - - +
20J LEU* 3.7 20.0 - - - +
21J PRO* 3.3 20.0 - - - +
56J VAL* 3.4 18.0 - - - +
63J LEU* 3.9 15.5 - - - -
64J ALA 3.5 4.5 - - - -
65J SER* 2.6 20.3 + - - -
96J VAL* 1.3 75.8 - - - +
98J THR* 1.3 64.2 + - - +
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Residues in contact with THR 98 (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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21J PRO* 4.4 2.7 - - - -
63J LEU* 3.5 9.7 - - - -
64J ALA* 2.8 40.8 + - - +
96J VAL* 4.5 14.1 - - + +
97J SER* 1.3 79.4 - - - +
99J VAL* 1.3 62.6 + - - +
100J ASP* 2.5 33.9 + - - +
101J GLY* 4.8 0.2 - - - -
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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