Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 5M9J
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 GLN 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.4 12.8 - - - +
83A LEU* 3.5 8.6 - - - +
84A HIS* 2.9 69.9 + - + +
85A GLY* 4.9 6.3 - - - -
91A PRO* 3.8 12.9 + - + +
92A CYS* 1.3 73.8 - - - +
94A TYR* 1.3 60.4 + - - +
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Residues in contact with TYR 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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23A ASP* 3.3 26.6 - - - +
26A CYS* 3.6 20.9 - - + -
27A GLU* 3.1 21.8 + - + +
30A MET* 3.3 42.1 - - + +
35A LEU 3.7 4.2 + - - -
36A THR* 4.5 1.6 - - + -
39A CYS* 3.8 6.1 - - - +
40A LYS 2.7 42.4 + - - -
81A CYS* 3.7 18.6 - - + -
82A LYS 3.4 19.1 - - - -
83A LEU* 3.5 14.1 - - + -
84A HIS* 4.0 3.1 + - - -
92A CYS* 3.4 33.6 - - + +
93A GLN* 1.3 71.2 - - - +
95A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 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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23A ASP* 3.4 19.5 + - - -
80A THR 3.4 3.5 - - - +
81A CYS* 3.6 1.0 - - - -
82A LYS* 2.8 43.7 + - + +
84A HIS* 3.1 52.1 + - + +
94A TYR* 1.3 72.6 - - - +
96A ALA* 1.3 62.9 + - - +
97A THR* 3.9 3.1 + - - +
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Residues in contact with ALA 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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21A ARG 3.5 15.0 - - - +
22A ASP* 3.3 35.9 - - - +
23A ASP* 2.9 11.6 + - - +
26A CYS* 3.5 14.6 - - - -
79A THR* 4.3 2.7 - - + -
80A THR 3.4 6.1 - - - +
94A TYR 4.0 0.6 - - - -
95A ARG* 1.3 73.0 - - - +
97A THR* 1.3 62.7 + - - +
98A ALA 4.1 0.6 + - - -
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Residues in contact with THR 97 (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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78A VAL* 5.4 0.7 - - - +
79A THR* 3.5 2.9 - - - -
80A THR* 2.8 50.3 + - - +
95A ARG* 4.8 3.5 + - - +
96A ALA* 1.3 74.0 + - - +
98A ALA* 1.3 71.3 + - - +
99A GLY* 3.8 1.0 + - - -
201A TLA 5.8 3.4 - - - +
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Residues in contact with ALA 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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21A ARG* 3.6 37.1 + - + +
78A VAL 3.4 6.7 - - - -
79A THR* 4.3 4.3 - - - +
96A ALA 4.1 1.4 - - - -
97A THR* 1.3 84.4 - - - +
99A GLY* 1.3 58.4 + - - +
201A TLA 4.5 5.5 + - - +
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Residues in contact with GLY 99 (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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21A ARG* 3.3 7.1 + - - +
77A GLN* 3.4 4.8 - - - +
78A VAL* 2.9 42.6 + - - +
97A THR* 3.8 1.2 + - - -
98A ALA* 1.3 76.5 - - - +
100A PHE* 1.3 60.1 + - - -
201A TLA 3.3 22.0 - - - -
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Residues in contact with PHE 100 (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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75A SER* 3.5 37.5 - - - -
76A PHE 3.2 17.0 - - - -
77A GLN* 3.5 31.6 - - + +
78A VAL* 4.4 0.2 - - - +
99A GLY* 1.3 73.9 - - - +
101A ARG* 1.3 60.5 + - - +
201A TLA 2.9 32.9 + - - +
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Residues in contact with ARG 101 (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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71A ILE* 4.7 9.1 - - - +
75A SER* 3.6 9.4 - - - -
76A PHE* 2.8 34.9 + - - +
78A VAL* 4.9 3.2 - - + +
99A GLY 4.3 0.2 - - - -
100A PHE* 1.3 78.5 - - - +
102A ASN* 1.3 99.6 + - - +
103A VAL* 4.0 2.4 - - - +
119A ILE* 3.8 35.2 + - - +
120A PHE* 3.9 24.9 - - + -
201A TLA 3.5 33.6 + - - +
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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