Contacts of the helix formed by residues 3119 - 3123 (chain C) in PDB entry 1HKN
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 ARG3119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2121B PRO 4.9 4.2 + - - -
3070C ASP* 4.4 6.7 + - - +
3071C GLY 3.5 7.4 - - - +
3072C LEU* 3.2 36.3 - - + -
3112C LYS* 5.5 0.6 - - - +
3117C CYS* 3.8 6.6 + - - +
3118C LYS* 1.3 75.2 - - - +
3120C GLY* 1.3 68.6 + - - +
3121C PRO* 3.2 35.3 - - + +
3122C ARG* 2.9 45.9 + - + +
3123C THR* 3.4 6.9 + - - +
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Residues in contact with GLY3120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3067C MET* 4.1 2.6 - - - +
3071C GLY 2.8 18.2 + - - -
3106C ASN 4.4 0.3 - - - +
3107C TRP* 3.3 32.5 - - - -
3108C PHE 3.9 14.8 - - - -
3118C LYS 3.5 1.4 + - - -
3119C ARG* 1.3 69.7 - - - +
3121C PRO* 1.3 65.4 - - - +
3123C THR* 2.7 23.1 + - - +
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Residues in contact with PRO3121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2106B ASN* 3.1 22.3 - - - +
2124B HIS* 3.6 30.5 - - + +
3070C ASP 3.6 19.1 - - - +
3071C GLY* 3.8 1.3 - - - -
3107C TRP* 3.3 27.3 - - + +
3119C ARG* 3.2 30.1 - - - +
3120C GLY* 1.3 89.0 - - - +
3122C ARG* 1.3 72.5 + - - +
3123C THR 3.4 0.2 - - - -
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Residues in contact with ARG3122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2105B LYS* 3.0 30.9 + - - +
2106B ASN* 3.2 11.4 + - - +
2107B TRP* 3.8 9.1 - - - +
2120B GLY 3.9 0.2 + - - -
2121B PRO* 3.1 32.5 + - - +
2122B ARG* 4.8 0.8 - - - +
2123B THR 3.1 29.9 + - - +
3118C LYS* 3.2 22.3 + - + +
3119C ARG* 2.9 47.9 + - + +
3121C PRO* 1.3 103.0 + - - +
3123C THR* 1.3 61.2 + - - +
3127C GLN* 3.0 18.7 + - - -
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Residues in contact with THR3123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2106B ASN* 3.6 15.4 - - - +
3106C ASN 3.7 4.5 + - - +
3108C PHE* 3.1 39.0 + - - +
3110C GLY* 4.8 2.5 - - - -
3118C LYS* 3.7 20.4 - - + +
3119C ARG 3.4 15.9 - - - +
3120C GLY 2.7 18.3 + - - +
3122C ARG* 1.3 80.6 - - - +
3124C HIS* 1.3 65.6 + - - +
3127C GLN* 3.2 5.8 - - - -
3130C ILE* 3.7 23.3 - - + -
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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