Contacts of the helix formed by residues 162 - 175 (chain J) in PDB entry 1S7X
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 GLY 162 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158J ALA 2.9 15.6 + - - -
159J TYR 3.2 1.6 + - - -
160J LEU 3.3 0.2 - - - -
161J GLU* 1.3 76.7 - - - +
163J GLU* 1.3 65.0 + - - -
164J CYS 3.3 0.7 - - - -
165J VAL* 3.2 4.0 + - - +
166J GLU* 2.9 34.6 + - - +
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Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J LYS* 4.7 1.0 + - - -
158J ALA 4.1 1.6 + - - -
159J TYR* 3.3 38.0 + - + +
162J GLY* 1.3 70.8 - - - -
164J CYS* 1.3 56.7 + - - +
166J GLU* 4.1 3.6 - - - -
167J TRP* 2.7 52.0 + - + +
1L LYS* 2.3 43.6 + - + +
2L ALA 4.6 2.4 - - - +
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Residues in contact with CYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J MET* 3.2 26.3 - - - +
100J GLY* 3.6 11.9 - - - -
101J CYS* 2.1 56.9 - - - -
159J TYR* 2.9 37.9 + - + +
160J LEU* 3.5 9.6 - - - +
163J GLU* 1.3 76.3 - - - +
165J VAL* 1.3 61.5 + - - +
168J LEU* 3.2 21.7 + - - +
1L LYS 5.2 0.2 - - - -
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Residues in contact with VAL 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J CYS* 4.3 3.8 - - - -
103J LEU* 4.2 13.5 - - + -
107J TRP 4.4 3.1 - - - +
108J ARG* 5.7 3.1 - - - +
109J LEU* 3.9 29.6 - - + +
160J LEU 3.4 19.3 - - - +
161J GLU 3.7 14.6 - - - +
162J GLY 3.2 6.6 + - - +
164J CYS* 1.3 72.7 - - - +
166J GLU* 1.3 72.7 + - - +
168J LEU* 3.2 4.3 + - - +
169J HIS* 3.0 52.2 + - + +
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Residues in contact with GLU 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J GLU 4.5 3.1 - - - +
162J GLY* 2.9 32.6 + - - +
163J GLU* 3.6 8.3 - - - +
165J VAL* 1.3 85.3 - - - +
167J TRP* 1.3 67.3 + - + +
169J HIS* 3.3 21.9 + - - +
170J ARG* 3.3 13.4 + - - +
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Residues in contact with TRP 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J MET* 4.6 2.2 - - + -
55J GLU* 4.4 0.9 - - - -
59J TYR* 3.8 20.2 - + - -
62J ARG* 3.7 25.1 - - - -
163J GLU* 2.7 38.9 + - + +
166J GLU* 1.3 75.9 - - + +
168J LEU* 1.3 59.1 + - - +
170J ARG* 3.1 51.2 + - - +
171J TYR* 3.0 54.6 + + + -
1L LYS* 3.6 47.0 - - + +
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Residues in contact with LEU 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J HIS* 4.6 0.2 - - + -
4J SER* 3.6 39.3 - - - +
5J MET* 3.9 16.5 - - + +
28J VAL* 3.7 25.1 - - + -
101J CYS* 4.2 6.7 - - - +
103J LEU* 3.2 41.5 - - + -
164J CYS 3.2 18.5 + - - +
165J VAL 3.2 4.6 + - - +
167J TRP* 1.3 74.7 - - - +
169J HIS* 1.3 63.2 + - - +
171J TYR* 3.2 6.5 + - - +
172J LEU* 3.0 37.3 + - + +
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Residues in contact with HIS 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J LEU* 3.8 15.0 - - + +
107J TRP* 2.9 65.0 + + + +
108J ARG* 6.3 0.9 - - - -
165J VAL* 3.0 35.4 + - + +
166J GLU* 3.3 17.0 + - - +
168J LEU* 1.3 74.7 - - - +
170J ARG* 1.3 64.1 + - - +
172J LEU* 3.2 14.2 + - + +
173J LYS* 3.3 27.1 + - - +
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Residues in contact with ARG 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J GLU* 3.2 38.0 + - - +
166J GLU 3.3 9.6 + - - +
167J TRP* 3.1 46.0 - - - +
169J HIS* 1.3 79.6 - - - +
171J TYR* 1.3 60.6 + - - +
172J LEU 3.6 0.2 + - - -
173J LYS* 3.9 8.7 + - - +
174J ASN* 2.9 37.4 + - - +
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Residues in contact with TYR 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J MET* 3.6 20.4 - - - -
28J VAL* 4.0 11.6 - - + +
33J PHE* 3.7 13.9 - + - -
51J TRP* 3.6 37.8 - + + -
52J MET* 4.1 4.9 - - - -
55J GLU* 4.0 19.1 - - - -
59J TYR* 2.6 36.7 + + - -
167J TRP* 3.0 44.8 + + - +
168J LEU* 3.2 6.2 + - - +
170J ARG* 1.3 76.4 - - - +
172J LEU* 1.3 65.0 + - - +
174J ASN* 3.4 9.1 + - - -
175J GLY* 3.4 11.6 + - - -
179J LEU* 6.0 1.2 - - - +
1L LYS* 2.8 31.3 + - - -
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Residues in contact with LEU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J HIS* 3.2 55.4 - - + +
28J VAL* 4.0 12.8 - - + -
29J ASP* 3.4 16.6 - - - +
103J LEU* 4.2 8.5 - - + -
107J TRP* 4.1 24.9 - - + -
168J LEU* 3.0 31.1 + - + +
169J HIS* 3.2 5.1 + - - +
171J TYR* 1.3 75.8 - - - +
173J LYS* 1.3 63.6 + - - +
175J GLY 3.8 1.4 - - - -
176J ASN* 3.3 32.2 + - - +
179J LEU* 4.8 6.2 - - + +
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Residues in contact with LYS 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J TRP* 4.1 25.1 - - + -
169J HIS* 3.3 24.8 + - - +
170J ARG* 4.2 8.5 - - - +
172J LEU* 1.3 77.9 - - - +
174J ASN* 1.3 67.7 + - - +
175J GLY 3.6 0.2 + - - -
176J ASN* 3.8 18.0 + - - +
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Residues in contact with ASN 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J TRP* 4.0 17.5 + - + +
54J GLN* 3.0 43.4 + - - +
55J GLU* 3.4 24.5 + - - -
170J ARG* 2.9 28.9 + - - +
171J TYR* 3.4 8.6 + - - +
172J LEU 3.3 0.4 - - - -
173J LYS* 1.3 83.6 - - - +
175J GLY* 1.3 58.2 + - - +
176J ASN 3.8 1.0 + - - -
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Residues in contact with GLY 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J TRP* 3.6 28.5 - - - +
171J TYR 3.4 8.3 + - - -
172J LEU 3.8 3.6 - - - -
174J ASN* 1.3 77.2 - - - +
176J ASN* 1.3 61.9 + - - +
177J ALA 3.5 2.0 - - - -
178J THR* 3.8 10.2 - - - -
179J LEU* 3.5 33.8 + - - +
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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