Contacts of the helix formed by residues 99 - 104 (chain B) in PDB entry 2CXN
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET 3.3 24.5 - - - +
85B PHE 4.2 1.1 - - - +
87B GLY* 4.0 10.3 - - - +
97B ALA* 4.3 5.8 - - + -
98B VAL* 1.3 75.6 - - - +
100B HIS* 1.3 65.2 + - - +
101B VAL* 3.0 17.3 - - + +
102B ALA* 3.0 18.3 + - + +
103B LEU* 3.6 1.6 + - - +
111B ILE* 3.7 32.5 - - + -
113B VAL* 3.4 33.4 - - + -
118B VAL* 4.5 8.3 - - + -
269B TRP* 3.0 42.6 + - + -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET* 4.3 16.2 - - - +
98B VAL* 3.5 30.3 - - + +
99B LEU* 1.3 75.2 + - - +
101B VAL* 1.3 71.8 + - + +
103B LEU* 3.1 27.1 + - + +
104B ARG* 3.3 30.8 - - - +
269B TRP 4.0 5.6 + - - +
270B VAL* 5.5 2.0 - - + -
271B GLY 5.5 1.2 + - - -
274B TYR* 3.5 58.6 - + + +
277B TRP* 4.4 0.4 - - + +
495B GLU* 3.8 23.4 + - - +
496B HIS* 4.7 5.2 + + - -
499B PHE* 6.3 0.6 - - - +
510B PHE* 3.9 8.9 - + - -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 4.6 6.1 - - + +
85B PHE* 3.9 39.9 - - + +
98B VAL 4.9 2.2 + - - +
99B LEU* 3.0 23.4 - - + -
100B HIS* 1.3 83.0 - - + +
102B ALA* 1.3 63.3 + - - +
104B ARG* 3.5 16.2 + - - +
105B ASN* 3.2 21.4 + - - +
111B ILE* 4.9 4.9 - - + -
301B HIS* 5.2 0.7 + - - -
304B ASP* 3.8 28.8 - - + +
496B HIS* 3.9 18.8 - - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 3.0 23.5 + - + +
101B VAL* 1.3 78.2 - - - +
103B LEU* 1.3 64.9 + - - +
105B ASN* 3.1 9.9 + - - -
111B ILE* 3.9 21.3 - - + -
118B VAL* 3.8 28.9 - - + -
119B MET* 3.3 20.5 - - - +
122B VAL* 3.8 3.5 - - + +
269B TRP* 4.3 4.9 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU 4.0 6.3 - - - +
100B HIS* 3.1 25.9 + - - +
102B ALA* 1.3 78.0 - - - +
104B ARG* 1.3 58.5 + - - +
105B ASN 3.9 0.3 + - - -
106B ARG* 5.4 0.5 + - - -
119B MET* 5.5 0.2 - - - +
122B VAL* 3.8 20.9 - - + +
126B LEU* 4.1 5.5 - - - +
267B TRP* 3.9 20.4 - - + -
269B TRP* 4.0 6.1 - - + -
270B VAL* 3.8 30.5 - - + -
274B TYR 4.1 4.0 - - - +
277B TRP* 3.9 23.3 - - + +
278B SER* 3.8 39.0 - - - +
297B LEU* 4.1 15.3 - - - +
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B HIS* 3.3 36.4 + - - -
101B VAL* 3.8 3.6 - - - +
103B LEU* 1.3 76.5 - - - +
105B ASN* 1.3 58.4 + - - +
106B ARG* 2.8 16.7 + - - +
277B TRP* 3.0 34.7 - - - +
297B LEU* 3.4 36.6 - - + +
300B ALA* 3.7 19.7 - - + +
301B HIS* 3.2 19.3 - - - +
304B ASP* 2.7 43.7 + - - +
492B ALA* 3.8 5.5 - - - +
495B GLU* 2.8 30.3 + - - -
496B HIS* 3.7 10.7 + - - -
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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