Contacts of the helix formed by residues 101 - 110 (chain A) in PDB entry 7JDW
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 GLU 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR 3.8 0.4 + - - -
100A TYR* 1.3 79.4 - - - +
102A LYS* 1.3 63.9 + - - +
103A TYR 3.0 1.4 + - - -
104A TRP* 3.2 43.2 + - + +
105A PRO* 3.6 8.7 - - - +
230A HIS 4.1 3.8 - - - +
231A SER* 3.6 27.1 - - - -
232A VAL* 3.1 38.1 + - - +
233A GLU* 6.0 0.5 - - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 2.9 5.6 + - + +
101A GLU* 1.3 81.3 + - - +
103A TYR* 1.3 101.8 + - + +
105A PRO* 3.9 12.8 - - - +
106A PHE* 5.6 0.3 - - - +
347A ASP 3.1 26.3 + - - -
348A ASP* 4.8 8.5 + - - +
349A HIS 4.9 0.4 + - - -
350A PRO* 5.6 0.4 - - - +
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 2.8 28.7 + + + +
102A LYS* 1.3 119.7 + - + +
104A TRP* 1.3 66.3 + - - +
105A PRO* 3.2 3.4 - - - -
106A PHE* 2.7 28.3 + - + +
107A TYR* 3.1 28.1 + - + -
349A HIS 4.1 2.4 + - - -
350A PRO* 3.8 10.0 - - + +
351A LEU* 3.1 43.7 + - + +
352A TRP* 3.7 33.7 - + + +
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Residues in contact with TRP 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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91A PHE* 3.4 27.7 - + + -
96A LYS* 3.3 51.7 + - + -
99A THR* 3.0 42.4 + - - -
100A TYR 3.4 8.1 + - - -
101A GLU* 3.2 28.5 + - + +
103A TYR* 1.3 76.8 - - - +
105A PRO* 1.3 65.9 - - + +
107A TYR* 3.1 3.7 + - - +
108A GLN* 2.9 36.6 + - - +
229A ILE* 4.1 13.5 - - + -
230A HIS* 3.5 37.5 - - - -
231A SER* 4.0 4.0 - - - -
232A VAL* 5.7 0.7 - - + -
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Residues in contact with PRO 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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101A GLU 3.6 10.1 - - - +
102A LYS 3.9 11.4 - - - +
103A TYR 3.4 0.9 - - - -
104A TRP* 1.3 95.8 - - + +
106A PHE* 1.3 59.2 + - - +
108A GLN* 3.0 22.5 + - - +
109A LYS* 3.1 24.4 + - - +
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Residues in contact with PHE 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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88A VAL* 3.6 31.6 - - + -
102A LYS 5.6 0.2 - - - +
103A TYR* 2.7 26.1 + - + +
105A PRO* 1.3 72.8 - - - +
107A TYR* 1.3 71.8 + + - +
109A LYS* 3.3 1.7 + - - -
110A GLN* 2.7 61.6 + - + +
115A PHE* 3.8 24.7 - + - -
116A PRO* 4.3 15.9 - - + -
352A TRP* 3.7 37.5 - + - -
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Residues in contact with TYR 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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88A VAL* 3.6 21.8 - - + -
89A PRO* 3.7 35.4 - - + -
91A PHE* 3.3 35.9 + + + +
95A VAL* 4.1 5.4 - - + -
99A THR* 3.7 19.5 - - + +
103A TYR* 3.1 34.2 + - + -
104A TRP* 3.5 4.3 - - - +
106A PHE* 1.3 84.9 - + - +
108A GLN* 1.3 60.3 + - - +
111A GLY* 2.9 29.3 + - - -
115A PHE* 4.8 2.5 - + - -
186A TRP* 6.1 0.2 - + - -
352A TRP* 2.7 41.6 + - + +
353A MET* 3.3 17.1 - - + +
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Residues in contact with GLN 108 (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 PHE* 3.3 34.5 - - + -
104A TRP* 2.9 19.8 + - - +
105A PRO* 3.0 29.6 - - - +
106A PHE 3.3 0.2 - - - -
107A TYR* 1.3 79.3 - - - +
109A LYS* 1.3 58.8 + - + +
111A GLY* 4.6 1.4 + - - -
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Residues in contact with LYS 109 (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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105A PRO 3.1 16.7 + - - +
106A PHE* 4.0 2.5 - - - +
108A GLN* 1.3 78.9 - - + +
110A GLN* 1.3 86.6 + - + +
111A GLY 3.4 3.0 + - - +
113A HIS* 3.7 22.8 + - - -
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Residues in contact with GLN 110 (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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88A VAL* 3.6 17.1 - - + +
106A PHE* 2.7 52.3 + - + +
109A LYS* 1.3 111.1 - - + +
111A GLY* 1.3 65.8 + - - +
112A GLY 3.2 0.3 + - - -
113A HIS* 2.8 45.4 + - - +
114A TYR 4.5 5.2 - - - +
116A PRO* 6.2 1.1 - - + -
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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