Contacts of the helix formed by residues 99 - 104 (chain A) in PDB entry 2CXO
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A MET 3.4 23.8 - - - +
85A PHE 4.1 4.0 - - - +
87A GLY* 3.9 9.6 - - - -
97A ALA* 4.0 6.5 - - + -
98A VAL* 1.3 75.8 - - - +
100A HIS* 1.3 65.6 + - - +
101A VAL* 3.0 15.3 - - + +
102A ALA* 3.0 19.0 + - + +
103A LEU 3.6 1.7 + - - -
111A ILE* 3.7 32.5 - - + -
113A VAL* 3.4 33.4 - - + -
118A VAL* 4.6 7.4 - - + -
269A TRP* 3.0 44.3 + - + -
270A VAL* 5.5 0.2 - - - -
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Residues in contact with HIS 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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84A MET* 4.3 14.4 - - - +
98A VAL* 3.5 29.4 - - + +
99A LEU* 1.3 75.8 + - - +
101A VAL* 1.3 72.2 + - + +
103A LEU* 3.2 24.9 + - + +
104A ARG* 3.2 29.4 - - - +
269A TRP 4.1 4.6 + - - +
270A VAL* 5.6 2.7 - - + +
271A GLY 5.5 1.4 + - - -
274A TYR* 3.5 57.4 - + + +
277A TRP* 4.3 1.6 - - + -
495A GLU* 3.6 24.7 + - - +
496A HIS* 4.7 7.2 + + - -
499A PHE* 6.3 0.4 - - - +
510A PHE* 3.9 10.3 - + - -
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Residues in contact with VAL 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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84A MET* 4.7 7.4 - - + +
85A PHE* 3.9 38.4 - - + -
98A VAL 5.0 1.6 - - - +
99A LEU* 3.0 22.0 - - + -
100A HIS* 1.3 84.7 - - + +
102A ALA* 1.3 62.2 + - - +
104A ARG* 3.6 16.0 + - - +
105A ASN* 3.3 21.9 + - - +
111A ILE* 4.8 6.0 - - + +
301A HIS* 5.2 0.5 + - - -
304A ASP* 3.7 29.4 - - - +
496A HIS* 3.8 19.7 - - + -
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Residues in contact with ALA 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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99A LEU* 3.0 22.4 + - + +
101A VAL* 1.3 77.8 - - - +
103A LEU* 1.3 65.7 + - - +
105A ASN* 3.2 17.4 + - - -
111A ILE* 3.9 15.0 - - + -
118A VAL* 3.8 30.1 - - + -
119A MET* 3.3 21.1 - - - +
122A VAL* 3.8 3.8 - - + +
269A TRP* 4.4 4.7 - - + -
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Residues in contact with LEU 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 LEU 3.9 5.6 - - - +
100A HIS* 3.2 21.7 + - - +
102A ALA* 1.3 80.0 - - - +
104A ARG* 1.3 57.0 + - - +
105A ASN 4.0 0.2 + - - -
106A ARG* 5.4 0.5 + - - -
122A VAL* 3.7 21.1 - - + +
126A LEU* 4.0 13.0 - - - +
267A TRP* 4.0 15.3 - - + -
269A TRP* 3.9 20.4 - - + -
270A VAL* 3.8 25.8 - - + -
274A TYR 4.1 4.5 - - - +
277A TRP* 3.8 23.9 - - + +
278A SER* 3.7 36.6 - - - +
297A LEU* 4.1 7.8 - - - +
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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
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100A HIS* 3.2 30.6 + - - -
101A VAL* 3.7 6.0 - - - +
102A ALA 3.2 0.2 - - - -
103A LEU* 1.3 76.9 - - - +
105A ASN* 1.3 58.2 + - - +
106A ARG* 2.9 17.3 + - - +
277A TRP* 3.0 34.5 - - - +
297A LEU* 3.3 37.2 - - + +
300A ALA* 3.7 19.6 - - + +
301A HIS* 3.1 20.4 - - - +
304A ASP* 2.7 42.8 + - - +
492A ALA* 3.7 7.0 - - - +
495A GLU* 2.8 30.1 + - - -
496A HIS* 3.7 14.3 + - - -
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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