Contacts of the helix formed by residues 89 - 98 (chain A) in PDB entry 3MDV
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PRO* 4.1 11.2 + - - +
87A VAL 3.9 0.4 - - - -
88A THR* 1.3 77.6 - - - +
90A PRO* 1.3 68.7 - - - +
91A GLU* 3.6 15.6 + - - +
92A SER* 3.1 19.9 + - - -
93A VAL* 3.1 23.6 + - - +
381A ASP* 2.8 34.0 + - - -
398A MET* 4.0 1.3 - - - -
404A TYR* 3.5 2.7 - - - -
424B ARG* 3.8 8.7 - - - -
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Residues in contact with PRO 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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89A SER* 1.3 84.9 - - - +
91A GLU* 1.3 62.0 + - - +
93A VAL* 3.3 0.9 + - + -
94A LYS* 2.9 25.2 + - - +
398A MET* 4.1 0.7 - - + -
404A TYR* 3.4 27.4 - - + +
424A ARG 3.3 23.1 - - - +
425A PHE* 3.3 26.5 - - + +
426A THR* 3.8 12.6 - - + -
91B GLU* 5.5 2.5 - - - +
424B ARG* 3.4 34.3 - - - +
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Residues in contact with GLU 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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89A SER* 3.6 4.4 - - - +
90A PRO* 1.3 82.9 - - - +
92A SER* 1.3 57.3 + - - +
94A LYS* 3.3 7.2 + - - +
95A LYS* 2.8 30.1 + - - +
381A ASP* 5.5 0.2 - - - +
90B PRO* 5.6 2.3 - - - +
91B GLU* 3.9 32.8 + - + +
94B LYS* 3.4 41.1 + - + +
424B ARG* 3.1 45.1 + - - +
425B PHE* 4.3 8.1 - - - -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.1 29.6 - - - -
89A SER* 3.1 11.6 + - - -
91A GLU* 1.3 77.4 - - - +
93A VAL* 1.3 63.5 + - - +
95A LYS* 4.4 5.6 - - - -
96A PHE* 3.1 34.2 + - - +
380A ILE* 3.0 28.4 - - - +
381A ASP* 3.1 14.1 + - - -
393A PHE* 3.9 0.7 - - - -
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Residues in contact with VAL 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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87A VAL 4.6 5.4 - - - +
89A SER 3.1 14.3 + - - +
90A PRO 3.3 7.8 + - - +
92A SER* 1.3 73.2 - - - +
94A LYS* 1.3 66.2 + - - +
97A LEU* 3.1 46.5 + - + +
98A MET* 4.7 0.3 - - - +
393A PHE* 4.2 21.3 - - + -
398A MET* 3.7 26.5 - - - -
425A PHE* 3.7 15.9 - - + +
428A PHE* 3.9 10.8 - - + -
432A LEU* 3.8 18.2 - - + -
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Residues in contact with LYS 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 PRO 2.9 16.6 + - - +
91A GLU* 3.6 6.7 - - - +
93A VAL* 1.3 75.1 - - - +
95A LYS* 1.3 66.3 + - - +
98A MET* 3.1 35.8 + - + +
424A ARG* 4.6 5.5 - - - +
425A PHE* 3.8 37.9 - - + -
89B SER* 4.4 0.6 + - - -
91B GLU* 3.2 45.2 + - + +
381B ASP* 3.0 26.2 + - - -
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Residues in contact with LYS 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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91A GLU 2.8 21.2 + - - +
92A SER* 3.9 7.0 - - - +
93A VAL 3.4 0.2 - - - -
94A LYS* 1.3 78.3 - - - +
96A PHE* 1.3 86.5 + - + +
98A MET 4.6 0.2 - - - -
99A SER* 3.8 20.1 - - - -
102A TYR* 3.6 26.6 - - + +
378A THR* 4.3 18.0 - - - +
379A LEU 5.2 4.6 + - - -
380A ILE* 6.2 0.2 - - - +
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Residues in contact with PHE 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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87A VAL* 4.9 1.3 - - + -
92A SER* 3.1 27.8 + - - +
95A LYS* 1.3 101.0 - - + +
97A LEU* 1.3 63.1 + - - +
99A SER 3.7 4.7 - - - +
102A TYR* 3.3 70.8 - + + +
372A ARG* 4.2 7.3 + - + +
374A LEU* 3.7 16.6 - - + -
378A THR* 4.9 2.9 - - + -
380A ILE* 3.6 47.8 - - + -
391A LEU* 3.8 16.6 - - + -
393A PHE* 3.5 24.5 - + + -
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Residues in contact with LEU 97 (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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93A VAL* 3.1 39.0 + - + +
96A PHE* 1.3 76.5 - - - +
98A MET* 1.3 59.2 + - + +
99A SER 3.3 7.1 + - - +
370A THR* 3.9 13.2 - - + -
372A ARG* 3.7 46.2 + - + +
393A PHE* 3.9 18.4 - - + -
428A PHE* 4.3 22.0 - - + -
432A LEU* 3.4 29.9 - - + +
433A GLY* 3.2 21.5 - - - -
434A HIS* 4.2 5.4 + - - -
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Residues in contact with MET 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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93A VAL 4.7 1.3 - - - +
94A LYS* 3.1 28.4 + - + +
95A LYS 4.6 0.2 - - - -
97A LEU* 1.3 78.2 - - + +
99A SER* 1.3 58.0 + - - +
425A PHE* 3.8 31.2 - - + -
432A LEU* 3.9 15.9 - - + -
433A GLY* 3.6 30.1 - - - +
434A HIS* 5.9 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