Contacts of the helix formed by residues 93 - 105 (chain A) in PDB entry 2Y01
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 LEU 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A VAL* 2.9 27.8 + - + +
91A GLY 3.6 0.6 - - - -
92A LEU* 1.3 93.2 - - + +
94A VAL* 1.3 65.3 + - - +
95A VAL 3.5 0.9 - - - -
96A PRO* 3.8 1.3 - - - -
97A PHE* 2.9 49.4 + - + +
117A TRP* 3.9 1.9 - - - -
120A LEU* 4.0 30.1 - - + -
402A Y01 4.7 11.4 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.2 4.6 + - + +
90A VAL* 3.2 32.0 + - + +
93A LEU* 1.3 78.7 - - + +
95A VAL* 1.3 62.9 + - - +
98A GLY* 3.2 8.7 + - - -
117A TRP* 2.8 31.5 + - + +
120A LEU* 4.1 36.1 - - + +
121A ASP* 4.1 10.5 - - + +
124A CYS* 4.6 1.8 - - - -
333A TYR* 3.6 42.1 - - + +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 3.6 24.5 - - + -
51A VAL* 4.2 13.2 - - + -
52A VAL* 3.8 18.8 - - + +
55A ILE* 4.2 9.9 - - + -
90A VAL* 2.7 40.0 + - + +
91A GLY* 4.7 2.7 - - - +
94A VAL* 1.3 70.8 - - - +
96A PRO* 1.3 70.0 - - + +
98A GLY* 3.2 1.0 + - - +
99A ALA* 2.8 23.0 + - - +
330A TRP* 4.3 6.9 - - + -
333A TYR* 3.9 28.5 - - + -
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Residues in contact with PRO 96 (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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52A VAL* 4.3 14.4 - - + -
90A VAL 3.7 2.0 - - - +
91A GLY 3.1 28.5 - - - +
92A LEU* 3.3 18.8 - - - +
93A LEU* 3.8 8.7 - - - +
95A VAL* 1.3 94.4 - - + +
97A PHE* 1.3 63.1 + - + +
99A ALA* 3.3 8.5 - - + +
100A THR* 3.2 26.1 + - - +
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Residues in contact with PHE 97 (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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92A LEU 5.6 0.2 - - - -
93A LEU* 2.9 44.5 + - + +
94A VAL 3.4 0.8 + - - -
95A VAL 3.2 0.8 - - - -
96A PRO* 1.3 78.4 - - + +
98A GLY* 1.3 64.5 + - - +
100A THR* 2.7 25.1 + - + -
101A LEU* 3.3 6.6 + - - +
107A TRP* 3.6 26.2 - + + -
109A TRP* 3.7 35.7 - + + -
113A LEU* 4.8 22.0 - - + -
117A TRP* 3.4 31.0 - + + +
120A LEU* 6.3 2.2 - - + -
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Residues in contact with GLY 98 (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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94A VAL 3.2 7.3 + - - -
95A VAL 3.2 5.0 + - - -
97A PHE* 1.3 75.9 - - - +
99A ALA* 1.3 59.6 + - - +
101A LEU* 3.0 10.4 + - - +
102A VAL* 2.9 31.0 + - - +
117A TRP* 3.7 22.5 - - - +
330A TRP* 4.0 17.3 - - - -
333A TYR* 5.6 1.1 - - - -
601A Y00 5.0 1.1 - - - -
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Residues in contact with ALA 99 (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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48A MET* 3.6 44.4 - - + -
52A VAL* 5.9 1.1 - - + -
95A VAL* 2.8 17.3 + - + +
96A PRO* 3.3 9.6 - - + +
98A GLY* 1.3 75.8 - - - +
100A THR* 1.3 59.0 + - + +
101A LEU 3.1 0.2 + - - -
102A VAL* 3.2 2.3 + - - +
103A VAL* 2.8 35.7 + - + +
330A TRP* 3.9 1.4 - - - -
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Residues in contact with THR 100 (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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96A PRO 3.2 14.1 + - - +
97A PHE* 2.7 19.1 + - - -
99A ALA* 1.3 76.4 - - + +
101A LEU* 1.3 57.5 + - - +
103A VAL* 4.1 4.5 - - - +
104A ARG* 3.2 34.3 + - + +
106A THR 3.9 4.1 + - - +
107A TRP* 5.2 0.3 - - - -
108A LEU* 5.0 7.6 - - + +
109A TRP* 3.0 42.5 + - + +
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Residues in contact with LEU 101 (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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97A PHE 3.3 7.1 + - - +
98A GLY* 3.0 9.3 + - - +
100A THR* 1.3 78.9 + - - +
102A VAL* 1.3 65.7 + - - +
105A GLY* 3.1 23.9 + - - -
106A THR* 3.5 33.2 - - - +
107A TRP* 3.7 20.4 - - + +
117A TRP* 4.1 25.8 - - + -
197A GLY 5.0 1.8 - - - +
199A CYS* 4.1 19.7 - - + +
200A ASP* 5.9 2.5 - - - +
504A 2CV 6.0 0.2 - - - +
601A Y00 4.3 24.5 - - + +
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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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40A TRP* 3.3 34.6 - - + -
44A MET* 4.1 17.7 - - + -
48A MET* 5.2 4.7 - - - -
98A GLY 2.9 18.1 + - - +
99A ALA* 3.8 4.9 - - - +
101A LEU* 1.3 76.9 - - - +
103A VAL* 1.3 65.2 + - + +
105A GLY* 3.8 5.4 + - - -
330A TRP* 3.6 24.0 - - + -
504A 2CV 3.9 35.0 - - + -
601A Y00 3.7 19.5 - - - +
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Residues in contact with VAL 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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40A TRP* 3.7 17.3 - - - -
41A GLU* 3.6 30.8 - - + +
44A MET* 4.1 15.3 - - + -
45A SER* 3.5 42.8 - - - +
48A MET* 4.3 8.1 - - + -
99A ALA* 2.8 24.8 + - + +
100A THR* 4.6 1.8 - - - +
102A VAL* 1.3 73.8 - - + +
104A ARG* 1.3 76.7 + - + +
105A GLY 3.7 0.2 + - - -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 4.0 26.3 + - - +
100A THR* 3.2 22.0 + - - +
103A VAL* 1.3 88.0 - - + +
105A GLY* 1.3 57.1 + - - +
106A THR* 3.2 14.1 + - - +
108A LEU* 4.4 38.5 - - + +
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Residues in contact with GLY 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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101A LEU* 3.1 18.9 + - - +
102A VAL 3.8 4.3 + - - -
103A VAL 3.5 2.6 + - - -
104A ARG* 1.3 75.9 - - - +
106A THR* 1.3 69.3 + - - +
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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