Contacts of the helix formed by residues 95 - 105 (chain A) in PDB entry 2BYL
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 PRO 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS* 5.6 7.2 - - + +
93A CYS 3.2 8.7 - - - +
94A HIS* 1.4 95.6 - - + +
96A LYS* 1.3 56.4 + - - +
98A VAL* 3.8 8.4 - - + +
99A ASN* 2.9 30.0 + - - +
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Residues in contact with LYS 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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94A HIS* 3.1 21.9 + - + +
95A PRO* 1.3 78.6 - - - +
97A ILE* 1.3 58.0 + - - +
99A ASN* 3.6 6.1 + - - +
100A ALA* 3.2 24.1 + - - +
335A ALA* 3.9 14.4 - - + +
338A GLU* 3.1 33.3 + - - -
339A VAL* 4.2 9.4 - - + -
342A GLU* 2.7 40.0 + - - +
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Residues in contact with ILE 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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90A GLN* 4.1 19.3 - - + -
91A GLY 5.9 0.2 - - - +
94A HIS* 2.9 26.7 + - + +
96A LYS* 1.3 73.6 - - - +
98A VAL* 1.3 65.9 + - - +
100A ALA* 3.2 3.5 + - - +
101A LEU* 3.0 18.7 + - - +
295A SER 3.7 14.8 - - - +
296A GLY* 4.2 10.3 - - - +
298A LEU* 3.6 17.4 - - + +
332A VAL* 3.5 32.2 - - + +
335A ALA* 4.0 9.0 - - + -
336A ALA* 3.6 31.4 - - + +
339A VAL* 4.1 7.9 - - + -
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Residues in contact with VAL 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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93A CYS* 3.8 23.6 - - + +
94A HIS 2.9 18.9 + - - +
95A PRO* 3.8 7.6 - - + +
97A ILE* 1.3 76.3 - - - +
99A ASN* 1.3 57.4 + - - +
101A LEU* 3.3 3.1 + - - +
102A LYS* 3.0 37.0 + - + +
298A LEU* 3.6 12.1 - - + +
105B VAL* 3.9 37.7 - - + +
106B ASP* 3.7 23.6 - - - +
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Residues in contact with ASN 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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95A PRO 2.9 20.2 + - - +
96A LYS* 3.7 7.6 - - - +
97A ILE 3.3 0.2 - - - -
98A VAL* 1.3 77.1 - - - +
100A ALA* 1.3 59.3 + - - +
102A LYS* 3.4 9.5 + - - +
103A SER* 3.0 35.5 + - - -
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Residues in contact with ALA 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 LYS 3.2 12.6 + - - +
97A ILE 3.2 9.8 + - - +
99A ASN* 1.3 81.3 - - - +
101A LEU* 1.3 63.2 + - - +
103A SER* 3.9 5.0 - - - -
104A GLN* 3.3 22.3 + - - +
331A ARG* 3.7 34.9 - - + +
332A VAL* 4.4 0.7 - - - -
335A ALA* 3.8 11.4 - - + -
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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 ILE 3.0 12.2 + - - +
98A VAL 3.3 6.9 + - - +
100A ALA* 1.3 75.9 - - - +
102A LYS* 1.3 64.0 + - + +
103A SER 3.2 0.3 + - - -
104A GLN 3.2 1.6 + - - -
105A VAL* 3.0 27.0 + - - +
298A LEU* 4.1 12.6 - - + +
299A TYR* 4.4 10.3 - - + -
328A LEU* 3.6 32.6 - - + +
332A VAL* 3.4 27.7 - - + +
101B LEU* 4.1 24.5 - - + -
105B VAL* 3.4 33.4 - - + -
299B TYR* 6.3 0.2 - - + -
328B LEU* 4.2 9.6 - - + -
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Residues in contact with LYS 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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98A VAL* 3.0 24.7 + - + +
99A ASN* 3.9 9.4 - - - +
101A LEU* 1.3 78.1 - - + +
103A SER* 1.3 60.6 + - - +
105A VAL* 3.4 15.9 - - - +
106A ASP* 3.3 20.8 - - - +
102B LYS* 3.8 31.3 + - + +
105B VAL* 3.7 23.6 - - + -
106B ASP* 2.7 37.1 + - - -
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Residues in contact with SER 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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99A ASN* 3.0 24.5 + - - -
100A ALA* 3.9 6.1 - - - -
102A LYS* 1.3 79.8 - - - +
104A GLN* 1.3 60.5 + - - +
105A VAL 3.7 0.2 + - - -
106A ASP* 3.8 8.4 + - - +
107A LYS* 3.2 35.5 + - - +
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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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100A ALA 3.3 8.1 + - - +
101A LEU 3.2 2.2 + - - -
103A SER* 1.3 74.3 - - - +
105A VAL* 1.3 60.4 + - - +
106A ASP 3.1 2.7 - - - -
107A LYS* 2.9 38.3 + - - +
108A LEU* 2.9 49.6 + - - +
118A ASN* 5.0 1.8 - - - +
119A VAL* 3.9 11.5 - - - +
327A PRO* 3.8 18.3 - - - +
328A LEU* 3.8 13.5 - - + -
331A ARG* 3.3 47.0 + - + -
63B GLU 4.6 2.6 + - - -
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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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101A LEU 3.0 15.0 + - - +
102A LYS* 3.4 21.5 - - - +
104A GLN* 1.3 77.2 - - - +
106A ASP* 1.3 59.2 + - - +
109A THR* 3.9 16.9 - - + +
328A LEU* 3.7 4.6 - - + +
93B CYS* 3.3 21.8 - - - -
98B VAL* 3.9 29.5 - - + +
101B LEU* 3.4 30.7 - - + -
102B LYS* 4.0 11.9 - - + -
298B LEU* 3.7 19.7 - - + -
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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