Contacts of the strand formed by residues 14 - 19 (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 SER 14 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A PRO* 5.8 3.0 + - - -
619A PRO 5.9 0.2 - - - -
620A LEU* 3.4 26.5 - - - +
623A TYR* 5.6 2.4 + - - -
765A ILE* 4.8 0.3 - - - +
766A ARG* 2.8 58.3 + - - +
12J LEU 3.5 4.4 + - - -
13J GLU* 1.3 71.8 - - - +
15J GLN* 1.3 67.2 + - - +
16J PHE* 4.7 1.4 - - - +
90J ASP 6.0 0.2 - - - -
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Residues in contact with GLN 15 (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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673A GLY* 4.2 15.2 - - - +
678A LEU* 5.1 0.4 - - - +
763A LEU* 3.5 18.0 - - + +
764A ILE 3.3 13.5 - - - +
765A ILE* 3.4 31.4 - - + +
13J GLU* 3.8 11.0 + - + +
14J SER* 1.3 81.5 + - - +
16J PHE* 1.3 66.4 + - - +
76J SER* 2.7 30.9 + - - -
88J THR* 4.3 3.8 + - - -
89J ALA* 3.5 17.6 - - + +
90J ASP 3.9 9.8 + - - +
91J ILE* 3.5 27.6 - - + +
92J CYS 4.9 0.5 + - - -
93J GLN* 5.4 0.3 + - - +
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Residues in contact with PHE 16 (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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620A LEU* 4.7 28.3 - - + -
762A PHE 4.0 0.5 - - - +
763A LEU* 4.3 0.9 - - - +
764A ILE* 3.3 62.1 + - + +
766A ARG* 4.3 15.3 - - + -
771A TYR* 4.5 12.1 - + - -
14J SER* 4.7 2.2 - - - +
15J GLN* 1.3 82.5 - - - +
17J ILE* 1.3 78.7 + - - +
18J LEU* 5.0 2.5 - - + -
45J ILE* 4.8 7.9 - - + -
47J LEU* 6.0 2.5 - - + -
67J LEU* 4.9 7.6 - - + -
91J ILE* 3.8 6.0 - - - +
93J GLN* 3.3 26.7 - - + +
95J LEU* 4.0 31.6 - - + -
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Residues in contact with ILE 17 (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* 4.9 5.2 - - + -
757A MET* 4.3 17.9 - - + -
761A ASP* 3.9 35.9 - - + +
762A PHE 3.6 11.2 - - - +
763A LEU* 4.9 5.4 - - + -
16J PHE* 1.3 78.6 - - - +
18J LEU* 1.3 61.4 + - - +
70J LEU* 4.3 11.0 - - + -
74J MET* 4.6 11.4 - - + -
91J ILE* 3.7 31.2 - - + -
93J GLN 2.9 10.3 + - - +
94J MET* 3.0 21.3 - - + +
95J LEU 2.8 26.2 + - - -
136J ILE* 5.0 2.9 - - + -
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Residues in contact with LEU 18 (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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760A THR 3.1 5.9 - - - +
761A ASP* 3.3 1.6 - - - -
762A PHE* 3.0 36.6 + - + +
764A ILE* 3.6 34.5 - - + -
773A ILE* 5.0 2.7 - - + -
16J PHE* 3.8 2.1 + - + -
17J ILE* 1.3 74.1 - - - +
19J ARG* 1.3 62.3 + - - +
20J LEU* 4.2 20.5 + - + +
43J LEU* 4.5 18.4 - - + -
45J ILE* 4.3 13.9 - - + -
56J VAL* 4.2 11.9 - - + -
95J LEU* 3.4 42.8 - - + +
97J SER* 4.5 1.3 - - - +
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Residues in contact with ARG 19 (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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758A PRO* 5.2 3.2 - - - +
760A THR* 3.3 19.4 + - - +
761A ASP* 3.1 31.2 + - - +
17J ILE 4.1 0.6 - - - -
18J LEU* 1.3 74.0 - - - +
20J LEU* 1.3 69.1 + - - +
94J MET* 3.6 22.8 - - + +
95J LEU 2.9 11.6 + - - +
96J VAL* 4.3 19.5 - - + +
97J SER* 2.9 31.2 + - - +
132J TRP* 3.3 34.2 - - - +
135J GLY 5.3 1.0 + - - -
136J ILE* 3.5 29.5 + - - +
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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
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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