Contacts of the helix formed by residues 112 - 126 (chain Z) in PDB entry 5WTI
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 112 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E C 3.5 15.0 + - - +
111Z GLY* 1.3 77.6 - - - +
113Z ALA* 1.3 60.5 + - - +
114Z ASN* 3.9 21.3 + - - +
115Z GLN* 3.3 27.8 + - + +
116Z LEU* 2.9 33.8 + - - +
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Residues in contact with ALA 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E C 2.8 12.9 + - - +
112Z GLU* 1.3 71.5 - - - +
114Z ASN* 1.3 54.2 + - - +
116Z LEU* 4.3 2.7 - - - -
117Z SER* 2.7 39.1 + - - -
221Z ILE* 3.3 28.9 - - + +
224Z LEU* 3.7 17.9 - - + +
225Z GLU* 3.5 23.3 - - + +
228Z LEU* 3.7 6.9 - - + +
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Residues in contact with ASN 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E C 4.8 1.0 + - - -
19E G 3.4 28.9 + - - +
20E G 3.4 41.8 + - + +
112Z GLU* 3.9 17.6 + - - +
113Z ALA* 1.3 77.6 - - - +
115Z GLN* 1.3 87.2 + - - +
117Z SER* 4.1 1.2 - - - -
118Z ASN* 3.0 34.0 + - - +
221Z ILE* 3.9 27.7 - - + +
225Z GLU* 5.5 0.2 + - - -
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Residues in contact with GLN 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E G 3.4 26.7 - - - +
10H C 3.2 51.2 + - + +
11H C 5.8 3.1 + - - -
112Z GLU* 3.3 33.5 + - + +
113Z ALA 3.2 0.4 - - - -
114Z ASN* 1.3 88.8 + - - +
116Z LEU* 1.3 61.4 + - + +
118Z ASN* 3.4 1.9 + - - +
119Z LYS* 2.9 31.2 + - - +
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Residues in contact with LEU 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Z GLU 3.4 23.8 - - - +
102Z LEU 3.2 20.6 - - - +
104Z PRO* 3.6 19.3 - - + -
111Z GLY* 4.1 4.3 - - - -
112Z GLU 2.9 41.4 + - - +
113Z ALA* 3.7 5.4 - - - +
115Z GLN* 1.3 77.3 - - + +
117Z SER* 1.3 58.5 + - - +
119Z LYS* 3.2 4.2 + - + -
120Z PHE* 2.9 52.9 + - + +
224Z LEU* 4.0 11.9 - - + -
228Z LEU* 4.2 7.6 - - + -
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Residues in contact with SER 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Z ALA 2.7 21.6 + - - -
114Z ASN 4.1 0.4 - - - -
116Z LEU* 1.3 74.3 - - - +
118Z ASN* 1.3 59.4 + - - +
121Z LEU* 2.9 41.1 + - - +
122Z TYR* 4.6 0.7 - - - -
217Z LYS* 3.9 4.7 + - - +
220Z PHE* 3.3 32.6 - - - +
221Z ILE* 3.5 25.1 - - - +
224Z LEU* 3.8 10.2 - - - +
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Residues in contact with ASN 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E G 2.8 30.2 + - - +
21E A 3.6 7.9 - - - +
8H T 4.2 8.7 - - + +
9H T 3.5 36.5 + - + +
10H C 4.4 0.2 - - - +
114Z ASN* 3.0 13.4 + - - +
115Z GLN 3.8 3.4 - - - +
116Z LEU 3.4 0.2 - - - -
117Z SER* 1.3 78.9 + - - +
119Z LYS* 1.3 60.5 + - - +
122Z TYR* 3.4 23.9 - - - +
131Z SER* 4.8 2.6 + - - -
217Z LYS* 3.6 28.8 + - - -
221Z ILE* 5.4 4.0 - - - +
398Z ASN* 3.7 8.9 + - - +
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Residues in contact with LYS 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H T 4.2 9.8 - - + +
10H C 6.0 1.3 - - + +
11H C 4.6 10.9 + - - +
101Z GLU* 5.0 3.4 + - - -
115Z GLN 2.9 19.2 + - - +
116Z LEU* 3.7 6.5 - - + +
117Z SER 3.1 0.2 - - - -
118Z ASN* 1.3 79.4 - - - +
120Z PHE* 1.3 89.7 + - + +
123Z PRO* 3.3 10.7 - - - +
131Z SER* 3.0 25.3 + - - +
169Z ASP* 2.9 35.9 + - - -
171Z LEU* 4.1 19.6 - - + +
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Residues in contact with PHE 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Z LEU* 4.3 14.4 - - + -
101Z GLU* 3.5 47.8 - - + -
102Z LEU* 3.5 26.9 - - + -
116Z LEU* 2.9 40.9 + - + +
119Z LYS* 1.3 104.2 - - + +
121Z LEU* 1.3 66.2 + - - +
122Z TYR 3.3 2.7 - - - -
123Z PRO* 3.2 4.4 - - - +
124Z LEU* 3.1 34.2 + - + +
171Z LEU* 3.5 36.8 - - + -
220Z PHE* 5.0 0.4 - - + -
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Residues in contact with LEU 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Z TYR* 4.9 5.6 - - + +
117Z SER* 2.9 22.1 + - - +
120Z PHE* 1.3 78.1 - - - +
122Z TYR* 1.3 68.0 + - + +
124Z LEU* 3.5 2.3 + - - -
125Z VAL* 3.2 45.5 + - + +
187Z PHE* 3.9 18.4 - - + -
189Z PRO* 5.9 0.9 - - + -
212Z VAL* 4.4 19.3 - - + -
216Z ASP* 4.3 4.0 - - + +
217Z LYS* 4.0 39.3 - - + +
220Z PHE* 3.9 34.0 - - + -
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Residues in contact with TYR 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H A 2.6 49.3 + - - -
8H T 3.4 54.6 - + + +
117Z SER 4.6 1.8 - - - -
118Z ASN* 3.4 28.0 - - - -
121Z LEU* 1.3 79.1 - - + +
123Z PRO* 1.3 65.5 - - + +
125Z VAL* 3.2 2.7 + - - -
126Z ASP* 2.8 34.5 + - - +
129Z SER* 3.6 4.5 - - - +
131Z SER* 5.0 1.6 - - - -
211Z SER* 3.9 17.9 - - - -
212Z VAL* 3.7 19.5 - - + -
217Z LYS* 3.3 27.8 + - + +
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Residues in contact with PRO 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Z LYS 3.3 22.9 - - - +
120Z PHE* 3.2 15.3 - - - +
122Z TYR* 1.3 95.0 - - + +
124Z LEU* 1.3 58.9 + - + +
125Z VAL 3.4 0.3 + - - -
126Z ASP 3.7 9.5 - - - +
129Z SER* 3.6 16.1 - - - +
131Z SER* 3.8 16.8 - - - +
133Z LYS* 5.9 0.2 - - - -
171Z LEU* 4.6 6.5 - - + -
175Z LEU* 3.7 34.5 - - + +
184Z ILE* 3.7 20.4 - - - +
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Residues in contact with LEU 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Z LEU* 3.8 37.9 - - + -
102Z LEU* 4.1 20.6 - - + -
120Z PHE* 3.1 30.0 + - + +
121Z LEU 4.0 2.9 - - - +
123Z PRO* 1.3 76.8 - - + +
125Z VAL* 1.3 59.2 + - - +
171Z LEU* 5.6 0.9 - - + -
175Z LEU* 4.1 14.4 - - + -
178Z LEU* 4.1 18.2 - - + -
184Z ILE* 4.6 1.8 - - + -
185Z PRO* 3.7 2.0 - - - +
186Z LEU* 2.7 38.9 + - + +
187Z PHE* 3.7 29.3 + - + -
220Z PHE* 5.1 1.8 - - + -
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Residues in contact with VAL 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Z LEU* 3.2 26.7 - - + +
122Z TYR* 3.2 1.3 + - - +
124Z LEU* 1.3 80.0 - - - +
126Z ASP* 1.3 63.7 + - + +
127Z PRO* 4.0 1.6 - - - +
185Z PRO* 3.2 24.2 - - - +
187Z PHE* 3.5 41.3 - - + +
189Z PRO* 3.4 33.7 - - + +
211Z SER 5.1 3.1 - - - +
212Z VAL* 3.8 15.9 - - + -
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Residues in contact with ASP 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Z TYR 2.8 14.2 + - - +
123Z PRO* 3.7 8.8 - - - +
125Z VAL* 1.3 80.3 - - + +
127Z PRO* 1.3 68.5 - - - +
128Z ASN* 2.6 42.6 + - - +
129Z SER* 3.2 25.6 + - - -
184Z ILE* 4.9 0.7 - - - -
211Z SER* 3.1 36.1 + - - +
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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