Contacts of the helix formed by residues 162 - 175 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G ALA 3.1 14.2 + - - -
159G TYR 3.3 0.2 + - - -
161G GLU* 1.3 78.6 - - - +
163G GLU* 1.3 54.5 + - - +
164G CYS 3.3 0.4 - - - -
165G VAL* 3.0 6.8 + - - +
166G GLU* 2.7 47.2 + - - +
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Residues in contact with GLU 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LYS* 4.8 0.2 - - - -
158G ALA 4.0 2.4 + - - -
159G TYR* 3.3 34.2 + - + +
162G GLY* 1.3 70.0 - - - +
164G CYS* 1.3 58.5 + - - +
166G GLU* 3.1 9.3 + - - -
167G TRP* 2.8 50.0 + - + +
1I LYS* 2.5 47.3 + - + +
2I ALA 4.3 1.4 - - - +
4I PHE* 5.8 2.9 - - - -
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Residues in contact with CYS 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G MET* 3.5 24.2 - - - +
100G GLY* 3.6 13.0 - - - -
101G CYS* 2.1 54.3 - - - -
159G TYR* 3.0 37.9 + - + +
160G LEU* 3.7 7.0 - - - +
163G GLU* 1.3 75.9 - - - +
165G VAL* 1.3 61.3 + - - +
168G LEU* 3.1 25.8 + - - +
1I LYS 5.0 0.2 - - - -
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Residues in contact with VAL 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CYS* 4.2 4.3 - - - -
103G LEU* 4.1 16.4 - - + -
107G TRP 4.5 1.8 - - - +
108G ARG* 5.8 0.2 - - - -
109G LEU* 4.1 26.7 - - + +
160G LEU 3.5 19.3 - - - +
161G GLU* 3.7 16.6 - - - +
162G GLY 3.0 7.8 + - - +
164G CYS* 1.3 73.6 - - - +
166G GLU* 1.3 67.4 + - - +
167G TRP 3.3 0.2 + - - -
168G LEU* 3.3 3.3 + - - +
169G HIS* 3.0 51.7 + - + +
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Residues in contact with GLU 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G GLY* 2.7 35.2 + - - +
163G GLU* 3.6 8.3 + - - +
165G VAL* 1.3 74.8 - - - +
167G TRP* 1.3 67.2 + - + +
169G HIS* 3.6 10.4 - - - +
170G ARG* 3.3 21.0 + - - +
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Residues in contact with TRP 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G MET* 4.4 2.9 - - + -
59G TYR* 4.0 17.7 - + - -
62G ARG* 3.7 22.4 - - - -
163G GLU* 2.8 35.9 + - + +
166G GLU* 1.3 80.9 - - + +
168G LEU* 1.3 59.3 + - - +
170G ARG* 2.9 51.1 + - - +
171G TYR* 2.8 57.1 + + + -
1I LYS* 3.4 47.4 - - + +
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Residues in contact with LEU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G HIS* 4.3 0.9 - - + -
4G SER* 3.6 44.6 - - - +
5G MET* 3.7 15.6 - - + +
28G VAL* 3.8 24.5 - - + -
101G CYS* 4.3 5.2 - - - +
103G LEU* 3.5 36.3 - - + -
164G CYS 3.1 19.7 + - - +
165G VAL* 3.3 4.2 + - - +
167G TRP* 1.3 77.0 - - - +
169G HIS* 1.3 63.0 + - - +
171G TYR* 3.2 7.4 + - - +
172G LEU* 2.9 39.0 + - + +
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Residues in contact with HIS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 3.5 16.1 - - + +
107G TRP* 2.7 63.5 + + + +
165G VAL* 3.0 33.7 + - + +
166G GLU* 3.6 12.5 - - - +
168G LEU* 1.3 77.5 - - - +
170G ARG* 1.3 63.7 + - - +
172G LEU* 3.2 11.2 + - - +
173G LYS* 3.2 26.5 + - - +
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Residues in contact with ARG 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G GLU* 2.8 39.2 + - - -
59G TYR* 4.6 1.6 - - - +
166G GLU 3.3 10.4 + - - +
167G TRP* 2.9 51.7 + - + +
169G HIS* 1.3 79.7 - - - +
171G TYR* 1.3 58.1 + - + +
173G LYS* 3.3 12.1 + - - +
174G ASN* 2.9 44.8 + - - +
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Residues in contact with TYR 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G MET* 3.6 22.0 - - - -
7G TYR* 4.1 0.2 + - - -
28G VAL* 4.0 12.6 - - + -
33G PHE* 3.5 17.9 - + - -
51G TRP* 3.7 30.4 - + + -
52G MET* 3.5 24.2 - - + -
55G GLU* 4.3 7.0 - - - -
59G TYR* 2.5 32.5 + + - -
167G TRP* 2.8 44.3 + + + +
168G LEU* 3.7 4.3 - - - +
170G ARG* 1.3 77.2 - - + +
172G LEU* 1.3 62.3 + - - +
174G ASN* 3.5 3.1 + - - -
175G GLY* 3.3 19.4 + - - +
1I LYS* 2.5 30.5 + - - -
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Residues in contact with LEU 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G HIS* 3.4 57.0 - - + +
28G VAL* 4.1 17.5 - - + -
29G ASP* 4.0 7.4 - - - +
103G LEU* 4.5 4.5 - - + -
107G TRP* 3.7 28.3 - - + -
168G LEU* 2.9 29.3 + - + +
169G HIS 3.5 7.2 - - - +
171G TYR* 1.3 75.7 - - - +
173G LYS* 1.3 61.1 + - - +
175G GLY 3.7 2.2 - - - +
176G ASN* 3.3 31.0 + - - +
179G LEU* 5.6 7.9 - - + +
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Residues in contact with LYS 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G TRP* 3.8 24.8 - - + -
169G HIS* 3.2 28.3 + - - +
170G ARG* 3.8 7.6 - - - +
172G LEU* 1.3 75.0 - - - +
174G ASN* 1.3 60.1 + - - +
175G GLY 2.9 11.4 + - - -
176G ASN* 3.4 19.4 + - - +
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Residues in contact with ASN 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G TRP* 4.4 16.2 - - + +
54G GLN* 3.4 28.9 + - - +
55G GLU* 3.1 29.5 + - - +
170G ARG* 2.9 41.8 + - - +
171G TYR* 3.5 12.2 + - - +
173G LYS* 1.3 76.1 - - - +
175G GLY* 1.3 56.5 + - - +
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Residues in contact with GLY 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TRP* 4.1 21.4 - - - -
171G TYR 3.3 11.7 + - - +
172G LEU* 3.7 5.4 - - - +
173G LYS 2.9 1.4 + - - -
174G ASN* 1.3 79.2 - - - +
176G ASN* 1.3 62.3 + - - -
177G ALA* 3.3 3.9 + - - -
178G THR* 3.9 4.4 + - - -
179G LEU* 3.5 26.9 + - - +
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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