Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 5MMB
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 ASN 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY* 5.7 2.4 - - - -
82A TRP 3.3 1.8 + - - -
83A PRO* 1.3 86.3 + - - +
85A MET* 1.3 67.4 + - - +
86A ARG 3.4 2.2 - - - -
87A LYS* 3.3 34.2 + - + +
88A ASP* 3.6 8.8 + - - +
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Residues in contact with MET 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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73A LEU* 3.7 21.5 - - + -
76A ILE* 3.6 33.7 - - + -
77A ALA* 5.1 8.1 - - - -
80A TYR 3.9 14.4 - - - +
81A TRP* 3.8 26.2 - - + +
82A TRP* 3.1 56.2 - - + +
83A PRO 3.5 0.2 - - - -
84A ASN* 1.3 72.2 - - - +
86A ARG* 1.3 65.0 + - - +
88A ASP* 2.9 16.6 + - - +
89A VAL* 3.0 15.8 + - + +
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Residues in contact with ARG 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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69A ARG* 4.2 19.1 - - + +
70A GLU* 2.6 43.8 + - - -
73A LEU* 3.2 41.7 - - + +
84A ASN 3.4 0.4 - - - -
85A MET* 1.3 79.2 - - - +
87A LYS* 1.3 57.8 + - - +
89A VAL* 3.5 8.7 - - + +
90A VAL* 2.8 36.9 + - + +
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Residues in contact with LYS 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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84A ASN* 3.3 30.7 + - + +
85A MET 3.1 0.4 + - - -
86A ARG* 1.3 78.2 - - - +
88A ASP* 1.3 65.7 + - - +
90A VAL* 3.6 5.3 + - - +
91A LYS* 3.1 22.9 + - - +
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Residues in contact with ASP 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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51A GLN* 5.4 6.8 + - - -
54A ARG* 4.9 9.9 + - - +
55A GLN* 6.3 0.7 - - - -
58A VAL* 3.7 24.6 - - + +
82A TRP* 2.9 30.8 + - + +
83A PRO 4.4 1.2 - - - +
84A ASN 3.6 7.6 + - - +
85A MET 2.9 7.6 + - - +
87A LYS* 1.3 79.8 - - - +
89A VAL* 1.3 63.0 + - - +
91A LYS* 3.5 17.4 + - - +
92A GLN* 3.4 17.3 + - - +
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Residues in contact with VAL 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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58A VAL* 3.8 10.3 - - + -
69A ARG* 3.9 24.0 - - + +
72A THR* 4.1 18.8 - - + -
73A LEU* 4.7 11.4 - - + -
76A ILE* 3.9 27.8 - - + -
82A TRP* 5.9 0.2 - - + -
85A MET* 3.0 20.0 + - + +
86A ARG* 3.0 14.1 + - + +
88A ASP* 1.3 75.6 - - - +
90A VAL* 1.3 65.6 + - - +
92A GLN* 3.1 13.2 + - - +
93A LEU* 3.1 31.3 + - + +
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Residues in contact with VAL 90 (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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69A ARG* 4.1 26.9 - - + +
86A ARG* 2.8 24.7 + - + +
87A LYS* 4.0 5.6 - - - +
89A VAL* 1.3 72.3 - - - +
91A LYS* 1.3 62.2 + - - +
93A LEU* 3.3 10.9 + - + +
94A GLY* 3.2 18.5 + - - -
374A HIS* 3.8 33.8 - - + +
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Residues in contact with LYS 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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55A GLN* 5.6 6.0 + - - -
87A LYS 3.1 17.7 + - - +
88A ASP* 3.6 19.3 + - - +
89A VAL 3.1 0.2 - - - -
90A VAL* 1.3 78.0 - - - +
92A GLN* 1.3 64.9 + - - +
94A GLY* 3.7 1.6 + - - -
95A ARG* 3.3 55.9 + - - +
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Residues in contact with GLN 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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55A GLN* 4.0 34.4 - - + +
58A VAL* 3.6 31.9 - - + +
59A LEU* 3.3 32.5 - - + +
62A HIS* 5.5 7.4 - - + -
88A ASP 3.4 4.8 + - - +
89A VAL 3.1 8.7 + - - +
91A LYS* 1.3 82.4 + - + +
93A LEU* 1.3 68.0 + - + +
95A ARG* 3.0 34.3 + - - +
96A CYS* 3.0 15.7 + - - +
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Residues in contact with LEU 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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62A HIS* 3.3 38.4 - - + +
67A THR 3.6 7.9 - - - +
68A GLY* 3.8 5.2 - - - +
69A ARG* 3.6 36.1 - - + +
72A THR* 4.6 1.6 - - - +
89A VAL* 3.1 22.5 + - + +
90A VAL* 3.3 9.4 + - + +
92A GLN* 1.3 76.7 - - + +
94A GLY* 1.3 60.1 + - - +
95A ARG 3.3 1.0 + - - -
96A CYS* 3.5 15.8 + - - +
99A CYS* 4.9 6.1 - - + +
100A LEU* 3.9 10.6 - - - +
374A HIS* 3.5 37.0 - - + +
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Residues in contact with GLY 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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90A VAL 3.2 12.2 + - - -
91A LYS 3.7 2.2 + - - -
92A GLN 3.2 0.2 - - - -
93A LEU* 1.3 75.6 - - - +
95A ARG* 1.3 61.3 + - - +
96A CYS 3.6 0.2 - - - -
100A LEU* 3.5 18.8 - - - +
373A SER 4.4 5.2 - - - -
374A HIS* 3.6 25.5 - - - -
375A GLN 5.1 5.2 - - - +
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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