Contacts of the helix formed by residues 102 - 107 (chain A) in PDB entry 3HJW
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.1 9.0 - - + -
95A ALA* 4.0 11.0 - - + -
99A ALA* 2.8 25.6 + - + +
101A ARG* 1.3 71.3 - - - +
103A VAL* 1.3 64.3 + - - +
104A GLN* 2.9 8.5 - - - -
105A ALA* 2.8 23.3 + - + +
106A LEU* 3.8 5.4 + - + +
246A MET* 4.3 13.0 - - + +
249A ALA* 4.0 22.4 - - + -
250A VAL* 5.2 6.1 - - + -
299A LEU* 3.8 23.6 - - + -
302A LEU* 5.1 2.9 - - + -
327A PHE* 3.5 27.3 - - + -
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Residues in contact with VAL 103 (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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79A GLY 3.6 24.5 - - - +
80A HIS 4.1 14.6 - - - +
81A GLY* 4.1 5.6 - - - +
93A PRO 5.1 0.9 - - - +
95A ALA* 3.9 11.0 - - + +
100A THR 3.2 19.7 + - - +
102A VAL* 1.3 78.8 - - - +
104A GLN* 1.3 53.3 + - - +
106A LEU* 2.7 34.9 + - + +
107A LEU* 2.8 33.5 + - + +
42D G 3.8 8.1 - - - +
43D C 3.6 27.4 - - - +
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Residues in contact with GLN 104 (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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101A ARG* 2.7 31.7 + - - +
102A VAL 2.9 1.0 - - - +
103A VAL* 1.3 79.5 - - - +
105A ALA* 1.3 56.7 + - - +
106A LEU 3.2 0.4 - - - -
107A LEU* 4.4 4.9 - - - -
108A PRO* 3.1 22.7 - - - +
289A LEU* 4.9 6.6 - - + +
302A LEU* 3.9 18.4 - - + +
325A LYS* 3.4 26.8 - - - +
327A PHE* 4.6 1.4 - - - -
43D C 3.3 23.6 + - - +
44D U 3.0 40.8 + - - +
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Residues in contact with ALA 105 (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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102A VAL* 2.8 13.3 + - + +
104A GLN* 1.3 80.0 - - - +
106A LEU* 1.3 60.2 + - - +
108A PRO* 3.9 7.1 - - - +
109A ALA* 4.0 4.9 - - - +
249A ALA 3.7 18.6 - - - +
250A VAL* 4.7 5.2 - - + -
252A HIS* 2.8 24.0 + - + -
253A LEU* 3.9 26.0 - - + +
289A LEU* 4.6 10.7 - - + +
302A LEU* 4.8 7.4 - - + -
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Residues in contact with LEU 106 (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 VAL* 5.2 3.1 - - + -
81A GLY* 5.3 4.9 - - - -
93A PRO* 3.8 22.2 - - + -
102A VAL* 5.5 0.9 - - + -
103A VAL* 2.7 29.1 + - + +
105A ALA* 1.3 80.9 - - + +
107A LEU* 1.3 58.1 - - - +
108A PRO* 3.1 2.7 - - - -
109A ALA* 2.6 31.1 + - - +
111A LYS* 3.3 10.9 + - - -
208A SER* 4.7 8.3 + - - +
209A GLY* 6.1 0.2 - - - -
210A PRO* 3.9 16.8 - - + -
211A PHE* 3.5 36.8 - - + -
249A ALA* 3.4 34.8 - - + +
252A HIS* 3.9 0.7 - - + -
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Residues in contact with LEU 107 (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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80A HIS 5.2 0.4 - - - +
81A GLY* 3.6 10.5 - - - -
82A GLY* 3.5 22.2 - - - +
103A VAL* 2.8 40.9 + - + +
104A GLN* 4.4 1.3 - - - +
106A LEU* 1.3 72.0 - - - +
108A PRO* 1.4 63.3 - - + +
111A LYS* 3.2 11.4 + - - +
179A ALA* 3.1 20.1 - - - +
42D G 3.8 18.8 - - - +
43D C 4.2 14.4 - - - +
8E C 5.0 5.6 - - - +
9E G 3.5 52.4 - - + +
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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