Contacts of the helix formed by residues 142 - 154 (chain C) in PDB entry 5W5T
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 ASP 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.8 5.0 - - - +
12A ARG* 2.7 46.7 + - - -
58C SER* 3.3 6.9 + - - -
141C MET* 1.3 71.0 - - - +
143C TYR* 1.3 63.5 + - - +
144C GLU* 3.1 11.4 + - - +
145C TYR* 3.3 42.8 + - + +
256C SER* 3.0 22.8 + - - +
258C VAL* 3.7 7.5 - - + +
298C TRP* 3.7 13.9 - - + -
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Residues in contact with TYR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 3.9 1.9 + - - -
54C ASN* 3.3 37.0 + - + +
55C ALA* 3.5 16.2 - - - -
58C SER* 2.8 29.3 + - - +
60C ILE* 4.1 17.7 - - + -
131C VAL* 4.5 15.0 - - + -
133C LEU* 3.3 40.0 - - + +
139C TYR* 2.7 23.6 + - - -
141C MET* 3.9 36.3 - - + -
142C ASP* 1.3 68.6 - - - +
144C GLU* 1.3 62.1 + - - -
145C TYR 3.1 0.7 - - - -
146C MET* 3.1 11.7 + - + +
147C LEU* 3.1 25.9 + - + +
209C ILE* 4.4 3.1 - - + -
211C VAL* 5.6 0.2 - - - +
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.0 23.7 - - + +
8A GLN 5.5 0.2 - - - +
9A PRO* 4.6 3.9 - - + +
12A ARG* 3.7 14.6 + - - +
9C PRO* 3.4 15.7 - - - +
10C LEU* 2.9 25.6 + - - +
11C ALA* 3.1 32.4 + - - +
58C SER* 4.4 5.8 - - - +
142C ASP* 3.1 16.0 + - - +
143C TYR* 1.3 77.4 - - - +
145C TYR* 1.3 63.7 + - + +
147C LEU* 3.3 7.3 + - - +
148C GLN* 3.0 43.5 + - + +
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.4 45.6 - - + +
8A GLN* 3.9 17.0 + - - +
142C ASP* 3.5 42.2 - - + +
143C TYR 3.1 0.2 - - - -
144C GLU* 1.3 80.7 - - + +
146C MET* 1.3 60.7 + - - +
148C GLN* 3.6 2.3 + - - +
149C GLN* 3.2 22.9 + - - +
251C HIS* 4.1 7.4 - + + -
255C ASP* 4.3 18.6 - - + +
256C SER* 3.8 19.7 - - - +
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Residues in contact with MET 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C MET* 3.9 17.0 - - + -
142C ASP 4.4 0.2 + - - -
143C TYR* 3.1 17.2 + - + +
145C TYR* 1.3 79.0 - - - +
147C LEU* 1.3 60.0 + - - +
149C GLN* 3.4 2.8 + - - +
150C HIS* 3.0 27.4 + - - +
158C THR* 3.1 46.1 - - + +
159C ILE 3.7 1.1 - - - -
160C GLY* 3.3 22.4 - - - +
209C ILE* 3.5 28.9 - - + +
211C VAL* 3.6 23.3 - - + +
251C HIS* 3.8 22.2 + - + +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.6 18.4 - - + -
11C ALA* 3.7 35.9 - - + +
14C ALA* 4.1 8.3 - - + -
60C ILE* 5.1 3.8 - - + -
129C TYR* 3.9 27.8 - - + -
131C VAL* 3.9 16.8 - - + -
143C TYR 3.1 20.0 + - - +
144C GLU* 3.6 12.1 - - - +
146C MET* 1.3 72.7 - - - +
148C GLN* 1.3 67.0 + - - +
150C HIS* 3.1 8.2 + - - +
151C VAL* 3.1 25.1 + - - +
211C VAL* 3.8 22.2 - - + -
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.3 27.6 + - + +
8C GLN 5.1 4.2 + - - -
9C PRO* 5.3 1.0 - - - +
10C LEU* 3.6 22.4 - - + +
144C GLU* 3.0 39.4 + - - +
145C TYR* 3.9 6.1 - - - +
147C LEU* 1.3 75.9 - - - +
149C GLN* 1.3 58.3 + - - +
151C VAL* 3.2 13.7 - - - +
152C ASP* 2.9 43.7 + - - +
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Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C TYR 3.2 15.3 + - - +
146C MET 3.7 4.7 - - - +
148C GLN* 1.3 77.3 - - - +
150C HIS* 1.3 55.1 + - - +
152C ASP* 3.9 5.8 - - - +
153C SER* 2.8 45.5 + - - +
158C THR* 4.1 7.4 + - + +
181C ASP* 5.6 0.6 - - - +
249C VAL* 3.4 19.0 - - - +
250C ALA 2.9 28.3 + - - -
251C HIS* 2.4 40.5 + - + +
252C ARG 4.7 0.3 + - - -
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Residues in contact with HIS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C TYR* 4.9 3.8 - + - -
146C MET 3.0 13.8 + - - +
147C LEU 3.1 9.2 + - - +
149C GLN* 1.3 78.0 - - - +
151C VAL* 1.3 66.0 + - + +
153C SER* 3.3 4.1 + - - -
154C GLY* 3.2 18.9 + - - -
155C ALA* 3.3 26.7 + - - +
156C ASP 3.8 15.0 - - - -
157C VAL* 3.8 2.0 - - - -
158C THR* 2.9 28.0 + - - +
211C VAL* 3.2 39.7 + - + -
212C PHE 3.6 3.1 - - - -
213C HIS* 3.0 49.1 + + - -
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.7 23.6 - - + -
129C TYR* 3.7 39.5 - - + +
147C LEU 3.1 11.6 + - - +
148C GLN* 3.2 15.5 - - - +
150C HIS* 1.3 79.7 - - + +
152C ASP* 1.3 77.4 + - - +
154C GLY* 3.6 7.7 + - - -
213C HIS* 4.5 10.8 - - + +
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C GLN* 2.9 34.3 + - - +
149C GLN* 3.9 6.1 + - - +
151C VAL* 1.3 87.5 - - - +
153C SER* 1.3 61.8 + - - +
154C GLY* 3.3 1.0 + - - -
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Residues in contact with SER 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLN* 2.8 30.7 + - - +
150C HIS* 3.3 5.2 + - - -
152C ASP* 1.3 74.1 - - - +
154C GLY* 1.3 60.6 + - - +
155C ALA* 3.1 26.2 + - - +
158C THR* 4.4 1.7 + - - -
247C LYS* 3.4 16.6 - - - -
249C VAL* 4.4 15.9 - - - +
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Residues in contact with GLY 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C HIS 3.2 7.8 + - - -
151C VAL* 3.6 6.4 + - - -
152C ASP 3.2 4.9 + - - -
153C SER* 1.3 77.9 + - - +
155C ALA* 1.3 64.7 + - - +
156C ASP* 4.7 3.5 - - - +
213C HIS* 5.9 3.1 - - - -
247C LYS* 4.2 7.7 - - - +
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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