Contacts of the helix formed by residues 174 - 188 (chain A) in PDB entry 1S13
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ILE* 3.5 7.8 - - - +
173A ALA* 1.3 82.0 - - - +
175A ALA* 1.3 66.3 + - - +
176A THR* 3.5 6.8 + - - -
177A LYS* 3.0 45.3 + - - +
178A PHE* 3.0 18.4 + - - +
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Residues in contact with ALA 175 (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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141A LEU* 4.0 26.0 - - + +
145A GLN* 5.1 12.6 - - - +
172A ILE* 3.9 12.9 + - + +
173A ALA 4.2 0.6 - - - -
174A SER* 1.3 71.4 + - - +
176A THR* 1.3 58.9 + - - +
178A PHE* 3.9 1.7 - - - +
179A LYS* 2.9 42.3 + - + +
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Residues in contact with THR 176 (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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174A SER* 3.1 7.9 + - - -
175A ALA* 1.3 79.7 - - - +
177A LYS* 1.3 70.7 + - + +
179A LYS* 3.8 9.7 - - - +
180A GLN* 3.1 26.2 + - - +
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Residues in contact with LYS 177 (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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174A SER* 3.0 36.3 + - - +
176A THR* 1.3 82.0 - - + +
178A PHE* 1.3 66.3 + - - +
180A GLN* 3.2 15.0 + - - +
181A LEU* 2.9 22.7 + - - +
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Residues in contact with PHE 178 (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 PHE* 3.8 30.7 - + - -
82A GLU* 3.9 17.9 - - + -
83A LEU* 3.7 38.4 - - + -
138A LEU* 4.7 2.7 - - + -
141A LEU* 3.8 14.4 - - + -
172A ILE* 3.5 29.8 - - + -
174A SER 3.0 16.5 + - - +
175A ALA 4.0 2.0 - - - +
177A LYS* 1.3 77.5 - - - +
179A LYS* 1.3 52.3 + - - +
181A LEU* 3.1 16.1 + - + +
182A TYR* 2.7 64.0 + + + +
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Residues in contact with LYS 179 (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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138A LEU* 3.9 19.0 + - + +
141A LEU* 4.2 17.9 - - + -
142A SER* 3.5 23.6 + - - +
175A ALA* 2.9 35.8 + - + +
176A THR* 3.8 8.7 - - - +
178A PHE* 1.3 76.3 - - - +
180A GLN* 1.3 55.7 + - - +
182A TYR* 3.0 7.3 + - - +
183A ARG* 2.7 67.5 + - - +
300A 2FH 2.8 29.2 + - - -
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Residues in contact with GLN 180 (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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176A THR* 3.1 16.4 + - + +
177A LYS* 3.4 15.6 - - - +
179A LYS* 1.3 78.4 - - - +
181A LEU* 1.3 59.3 + - - +
183A ARG* 3.5 12.0 + - - +
184A SER* 3.0 27.4 + - - -
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Residues in contact with LEU 181 (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 PHE* 4.0 27.4 - - + -
177A LYS 2.9 12.8 + - - +
178A PHE* 3.4 20.4 - - + +
180A GLN* 1.3 76.0 - - - +
182A TYR* 1.3 59.0 + - - +
184A SER* 3.2 10.2 + - - -
185A ARG* 2.9 47.6 + - + +
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Residues in contact with TYR 182 (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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74A PHE* 4.9 0.2 - - - -
77A VAL* 3.6 35.4 + - + +
79A PHE* 3.8 11.2 - + - -
83A LEU* 3.9 18.2 - - + -
130A VAL* 5.1 0.9 + - + +
133A ALA* 3.4 31.7 + - - +
134A TYR* 4.1 9.1 + - + -
137A TYR* 4.3 4.8 - - + -
138A LEU* 3.6 37.7 - - + -
178A PHE* 2.7 45.4 + + + +
179A LYS 3.5 3.8 - - - +
181A LEU* 1.3 71.1 - - - +
183A ARG* 1.3 61.2 + - - +
185A ARG* 3.3 5.9 + - - +
186A MET* 2.9 52.1 + - + +
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Residues in contact with ARG 183 (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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14A SER* 3.6 27.8 + - - +
18A LYS* 3.5 28.2 - - - +
134A TYR* 5.9 0.9 - - + -
138A LEU* 4.3 13.2 - - + +
176A THR 5.8 0.2 + - - -
179A LYS* 2.7 51.3 + - - +
180A GLN* 3.8 8.8 - - - +
182A TYR* 1.3 72.4 - - - +
184A SER* 1.3 54.5 + - - +
186A MET* 3.2 9.9 + - - +
187A ASN* 2.8 41.5 + - - +
300A 2FH 2.6 39.6 + - - -
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Residues in contact with SER 184 (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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180A GLN* 3.0 16.1 + - - -
181A LEU* 3.2 18.1 + - - -
183A ARG* 1.3 77.1 - - - +
185A ARG* 1.3 63.4 + - - +
187A ASN* 3.2 9.8 + - - +
188A SER* 3.0 22.6 + - - -
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Residues in contact with ARG 185 (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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75A ALA 4.7 1.8 + - - -
76A PRO* 2.7 58.7 + - - +
77A VAL* 3.8 8.3 - - + -
78A TYR 5.1 3.0 + - - -
79A PHE* 3.3 33.3 - - + -
181A LEU* 2.9 31.1 + - + +
182A TYR 3.7 7.4 - - - +
183A ARG 3.3 0.2 - - - -
184A SER* 1.3 74.3 - - - +
186A MET* 1.3 66.7 + - - +
188A SER* 2.7 25.9 + - - -
189A LEU* 3.4 10.6 + - - +
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Residues in contact with MET 186 (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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13A LEU* 3.8 22.3 - - + +
14A SER* 4.7 9.4 - - - -
17A LEU* 3.4 33.4 - - + -
77A VAL* 3.9 18.6 - - + -
130A VAL* 4.9 10.3 - - + +
134A TYR* 3.5 34.8 - - + -
138A LEU* 4.3 2.9 - - - -
182A TYR* 2.9 39.6 + - + +
183A ARG* 3.3 15.5 - - - +
185A ARG* 1.3 75.8 - - - +
187A ASN* 1.3 61.9 + - - +
189A LEU* 3.1 30.0 + - + +
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Residues in contact with ASN 187 (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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12A ASP* 3.7 24.8 - - + +
13A LEU* 3.0 14.2 + - - +
14A SER* 2.8 47.3 + - - -
183A ARG* 2.8 25.9 + - - +
184A SER* 3.7 8.7 - - - +
186A MET* 1.3 75.4 - - - +
188A SER* 1.3 58.4 + - - +
189A LEU 3.2 5.7 + - - +
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Residues in contact with SER 188 (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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76A PRO* 3.9 14.1 - - - +
184A SER 3.0 12.3 + - - -
185A ARG* 2.7 26.4 + - - -
187A ASN* 1.3 76.2 - - - +
189A LEU* 1.3 64.4 + - - +
190A GLU* 3.4 13.1 + - - +
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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