Contacts of the helix formed by residues 101 - 107 (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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LEU 3.9 7.8 + - - -
84A ASP* 3.5 22.7 + - + +
85A ALA 3.3 13.5 - - - +
86A SER* 4.5 3.4 - - - +
87A VAL* 3.9 3.6 - - - -
99A ARG 3.4 15.9 - - - +
100A ILE* 1.4 73.9 - - - +
102A VAL* 1.3 65.4 + - - +
103A ARG* 3.6 5.2 + - - +
104A GLN* 2.9 37.0 + - - +
105A VAL* 3.0 24.8 + - - +
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Residues in contact with VAL 102 (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* 5.2 0.9 - - + -
81A LEU* 4.0 25.6 - - + -
82A ASP 4.1 3.4 - - - +
83A LEU* 3.6 17.5 - - + +
85A ALA 3.1 13.4 + - - +
87A VAL* 4.2 11.4 - - + -
90A TYR* 4.1 13.7 - - + -
101A THR* 1.3 74.7 - - - +
103A ARG* 1.3 63.8 + - - +
105A VAL* 3.2 5.2 + - + +
106A MET* 2.9 43.7 + - + +
170A LEU* 4.0 30.3 - - + -
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Residues in contact with ARG 103 (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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83A LEU* 2.8 52.4 + - + +
84A ASP* 2.8 41.7 + - - +
101A THR* 3.3 3.8 - - - +
102A VAL* 1.3 73.5 - - - +
104A GLN* 1.3 61.0 + - + +
106A MET* 3.3 2.2 + - - +
107A SER* 2.8 27.4 + - - -
109A ARG* 4.0 17.5 - - - +
267A GLN* 2.8 34.3 + - - +
270A GLN* 3.6 14.7 + - - -
282A LEU* 3.8 23.5 - - + +
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Residues in contact with GLN 104 (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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99A ARG 3.5 6.2 + - - +
100A ILE* 3.3 12.5 - - - +
101A THR* 2.9 39.1 + - - +
103A ARG* 1.3 75.5 - - + +
105A VAL* 1.3 65.3 + - - +
107A SER* 3.3 5.8 + - - -
108A HIS 3.2 3.5 + - - -
109A ARG* 2.8 51.4 + - - +
110A SER* 3.5 5.6 + - - +
153A PRO* 3.5 14.6 + - - +
154A GLY* 3.5 32.5 + - - +
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Residues in contact with VAL 105 (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 18.6 - - + -
95A LEU* 5.0 0.2 - - + -
100A ILE* 3.8 14.8 - - + -
101A THR 3.0 14.2 + - - +
102A VAL* 3.6 9.9 - - + +
104A GLN* 1.3 75.5 - - - +
106A MET* 1.3 68.6 + - + +
107A SER 3.2 1.0 + - - -
108A HIS 3.2 6.8 + - - -
110A SER* 3.9 1.6 - - - -
112A LEU* 4.5 5.6 - - + -
163A ASN* 3.0 71.4 - - - +
164A PHE* 4.0 2.0 - - + -
166A VAL* 4.1 15.5 - - + -
167A ALA* 4.8 3.6 - - + +
170A LEU* 5.8 2.5 - - + -
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Residues in contact with MET 106 (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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69A ALA* 3.7 39.5 - - + +
72A LEU* 3.8 32.8 - - + -
73A LEU* 4.2 8.5 - - + -
83A LEU* 3.8 27.8 - - - -
102A VAL* 2.9 24.9 + - + +
103A ARG 3.9 4.0 - - - +
104A GLN 3.3 0.4 - - - -
105A VAL* 1.3 80.6 - - + +
107A SER* 1.3 56.9 + - - +
108A HIS 3.5 0.4 - - - -
164A PHE* 3.5 19.4 - - + -
167A ALA* 5.7 0.4 - - + -
280A TYR* 3.5 5.0 - - - -
282A LEU* 4.0 23.1 - - + -
283A GLY 3.0 25.5 + - - -
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Residues in contact with SER 107 (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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103A ARG 2.8 20.0 + - - -
104A GLN 3.4 3.8 + - - -
105A VAL 3.1 0.2 - - - -
106A MET* 1.3 76.1 - - - +
108A HIS* 1.3 71.3 + - - +
109A ARG* 2.8 37.2 + - - +
157A TYR* 3.7 11.1 - - - -
270A GLN 5.9 0.7 - - - -
272A THR* 4.2 10.2 + - - -
280A TYR* 4.1 4.6 - - - +
281A GLY 3.2 21.8 - - - -
282A LEU* 4.1 6.1 - - - -
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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