Contacts of the helix formed by residues 160 - 176 (chain A) in PDB entry 1YQS
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A HIS* 3.1 17.9 + - - -
112A LEU 2.9 28.7 + - - -
114A ASP* 3.3 15.1 - - - -
158A SER* 3.2 5.4 + - - -
159A TYR* 1.3 79.8 - - - +
161A ASN* 1.3 63.9 + - - +
162A THR* 3.3 21.1 + - - -
163A ASN* 3.0 31.7 + - - +
164A PHE 4.2 0.3 + - - -
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Residues in contact with ASN 161 (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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62A SER* 5.3 0.9 - - - -
65A LYS* 3.0 30.7 + - - +
114A ASP* 2.9 32.3 + - - +
115A TYR* 3.7 19.7 - - + +
116A THR* 3.4 21.1 + - - +
159A TYR* 4.3 8.4 - - - -
160A SER* 1.3 71.0 - - - +
162A THR* 1.3 62.0 + - - +
164A PHE* 3.0 13.7 + - - -
165A VAL* 3.1 13.2 + - - +
233A TRP* 4.5 13.2 - - - -
234A ALA* 5.2 0.6 - - - +
237A ALA* 3.8 12.1 - - + +
400A BSA 6.0 0.8 - - - +
401A BSA 4.9 7.7 + - - -
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Residues in contact with THR 162 (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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95A LEU* 6.1 0.2 - - + -
112A LEU* 4.1 18.8 - - + -
113A TYR 2.7 22.0 + - - -
114A ASP* 3.7 0.9 + - - -
115A TYR* 3.2 25.1 - - + -
141A ILE* 3.9 20.6 - - + -
144A SER* 3.5 24.5 - - - +
145A LEU* 6.3 0.2 - - + -
160A SER* 3.3 9.4 + - - -
161A ASN* 1.3 78.3 - - - +
163A ASN* 1.3 62.1 + - - +
165A VAL* 3.2 4.8 + - - +
166A VAL* 3.0 21.4 + - - +
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Residues in contact with ASN 163 (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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105A VAL* 3.0 51.5 - - - +
108A HIS* 3.1 33.1 + - - +
110A SER* 2.6 35.2 + - - -
112A LEU* 3.7 11.7 - - - +
158A SER 4.4 0.7 - - - +
160A SER* 3.0 20.7 + - - +
162A THR* 1.3 78.6 - - - +
164A PHE* 1.3 61.5 + - + +
166A VAL* 3.4 3.6 - - - +
167A ALA* 3.1 14.4 + - - +
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Residues in contact with PHE 164 (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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65A LYS* 3.4 51.4 - - + -
68A SER* 3.9 8.3 - - - -
69A ALA* 4.2 11.9 - - + -
72A LEU* 5.2 0.2 - - + -
105A VAL* 4.0 1.6 - - + -
106A MET* 3.5 44.4 - - + -
108A HIS* 3.9 21.3 - + - -
161A ASN 3.0 4.4 + - - -
163A ASN* 1.3 77.2 - - - +
165A VAL* 1.3 57.4 + - - +
167A ALA* 3.4 20.7 - - + +
168A GLY 3.2 7.8 + - - -
236A SER* 2.7 27.9 + - - +
237A ALA* 3.7 28.0 - - + -
280A TYR* 4.3 0.7 - - - -
283A GLY* 3.7 15.7 - - - -
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Residues in contact with VAL 165 (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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115A TYR* 3.3 31.4 - - + +
137A TYR* 3.4 43.1 - - + +
140A LEU* 3.8 19.5 - - + -
141A ILE* 3.7 15.3 - - + -
161A ASN 3.1 9.7 + - - +
162A THR* 3.5 8.3 - - - +
164A PHE* 1.3 73.7 - - - +
166A VAL* 1.4 66.1 + - - +
168A GLY 3.1 2.8 + - - -
169A MET* 3.0 19.1 + - - +
234A ALA 4.2 11.0 - - - +
236A SER* 4.0 5.2 - - - -
237A ALA* 4.7 0.4 - - + -
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Residues in contact with VAL 166 (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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87A VAL* 3.8 29.6 - - + -
91A LEU* 4.7 0.4 - - + -
94A LEU* 4.3 12.8 - - + -
95A LEU* 4.6 2.9 - - + -
105A VAL* 4.1 14.1 - - + -
112A LEU* 4.2 20.6 - - + -
141A ILE* 3.6 20.0 - - + -
162A THR 3.0 18.2 + - - +
163A ASN 3.4 8.5 + - - +
165A VAL* 1.4 74.6 - - - +
167A ALA* 1.4 64.5 + - - +
169A MET* 3.1 10.6 + - - +
170A LEU* 2.9 32.8 + - + +
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Residues in contact with ALA 167 (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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68A SER* 4.5 7.2 - - - -
72A LEU* 3.6 27.7 - - + +
105A VAL* 5.4 2.9 - - + -
106A MET* 5.7 0.4 - - + -
163A ASN 3.1 9.4 + - - +
164A PHE* 3.4 35.2 - - + +
165A VAL 3.2 0.4 - - - -
166A VAL* 1.4 76.6 - - - +
168A GLY* 1.4 57.3 + - - +
170A LEU* 3.3 8.6 + - - +
171A ILE* 3.0 34.4 + - - +
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Residues in contact with GLY 168 (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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137A TYR* 3.9 10.3 - - - -
164A PHE 3.2 4.9 + - - -
165A VAL 3.1 5.4 + - - -
167A ALA* 1.4 75.4 - - - +
169A MET* 1.3 64.1 + - - +
171A ILE* 3.3 3.6 + - - +
172A GLU* 3.0 29.6 + - - +
179A VAL* 4.0 9.6 - - - -
236A SER* 3.2 25.5 + - - -
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Residues in contact with MET 169 (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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91A LEU* 3.7 20.3 - - + +
94A LEU* 3.7 29.2 - - + -
137A TYR* 3.3 28.9 - - + -
138A GLN* 3.9 26.9 - - + +
141A ILE* 3.6 27.4 - - - -
165A VAL 3.0 11.2 + - - +
166A VAL* 3.5 7.0 - - - +
168A GLY* 1.3 75.5 - - - +
170A LEU* 1.3 59.7 + - - +
172A GLU* 4.1 4.1 - - - +
173A LYS* 2.9 31.5 + - - +
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Residues in contact with LEU 170 (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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72A LEU* 4.1 17.7 - - + -
81A LEU* 4.9 2.0 - - + -
87A VAL* 4.6 6.3 - - + +
90A TYR* 3.7 39.7 - - + -
91A LEU* 3.7 17.9 - - + -
102A VAL* 4.0 31.9 - - + -
105A VAL* 5.8 2.2 - - + -
166A VAL* 2.9 30.6 + - + +
167A ALA* 3.5 9.4 - - - +
169A MET* 1.3 73.6 - - - +
171A ILE* 1.3 66.7 + - - +
173A LYS* 4.6 2.2 - - + -
174A LEU* 2.9 37.6 + - + +
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Residues in contact with ILE 171 (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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68A SER* 3.8 34.8 - - - +
71A VAL* 3.8 26.0 - - + -
72A LEU* 3.7 16.2 - - + -
75A LEU* 4.5 8.1 - - + -
167A ALA 3.0 24.2 + - - +
168A GLY* 3.3 6.5 + - - +
170A LEU* 1.3 75.2 - - - +
172A GLU* 1.3 63.0 + - - +
175A THR* 2.8 33.8 + - + +
179A VAL* 4.1 22.4 - - + -
182A GLU* 3.8 27.6 - - + -
183A TYR* 5.0 2.7 - - + -
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Residues in contact with GLU 172 (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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137A TYR* 3.9 24.8 - - - -
168A GLY 3.0 19.0 + - - +
169A MET* 4.1 3.8 - - - +
171A ILE* 1.3 76.3 - - - +
173A LYS* 1.3 57.3 + - - +
176A GLY* 2.9 29.8 + - - -
177A HIS 3.3 17.6 + - - +
178A SER* 3.5 10.4 - - - -
179A VAL* 2.9 38.4 + - + +
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Residues in contact with LYS 173 (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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90A TYR 3.9 23.2 + - - +
91A LEU* 3.9 14.8 - - + -
92A PRO* 6.0 2.2 - - - -
169A MET 2.9 18.8 + - - +
170A LEU* 3.9 3.8 - - + +
172A GLU* 1.3 81.6 - - - +
174A LEU* 1.3 73.9 + - + +
176A GLY* 3.7 5.7 + - - -
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Residues in contact with LEU 174 (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 LEU* 4.5 15.3 - - + -
80A LYS* 3.7 37.2 - - + +
81A LEU* 3.9 27.4 - - + -
90A TYR* 3.9 33.2 - - + +
170A LEU* 2.9 27.9 + - + +
171A ILE 4.4 0.9 - - - +
173A LYS* 1.3 89.0 - - + +
175A THR* 1.3 60.5 + - - +
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Residues in contact with THR 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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71A VAL* 5.5 0.2 - - + -
75A LEU* 3.8 32.3 - - + -
80A LYS* 5.8 3.4 - - + +
171A ILE* 2.8 22.0 + - + +
174A LEU* 1.3 79.3 - - - +
176A GLY* 1.3 59.0 + - - +
177A HIS* 3.1 41.6 + - - +
182A GLU* 3.6 34.8 - - + +
186A ARG* 4.8 2.2 - - - +
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Residues in contact with GLY 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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172A GLU 2.9 14.7 + - - -
173A LYS 3.7 5.1 + - - -
174A LEU 3.6 1.6 - - - -
175A THR* 1.3 76.8 - - - +
177A HIS* 1.3 66.8 - - - +
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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