Contacts of the strand formed by residues 3132 - 3136 (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 PHE3132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3014C LEU* 3.9 27.1 - - + -
3015C TYR 3.2 3.1 - - - -
3016C CYS* 3.5 31.9 - - + -
3023C LEU* 4.2 20.9 - - + -
3094C TYR* 3.3 4.6 - - - -
3095C ASN* 2.6 43.0 + - - +
3097C TYR* 4.3 24.0 - + + -
3109C VAL* 3.3 43.1 - - + -
3110C GLY* 4.0 6.3 - - - -
3111C LEU* 4.2 11.2 - - + -
3129C ALA 3.7 15.3 - - - -
3130C ILE 3.3 13.2 - - - -
3131C LEU* 1.3 70.9 - - - +
3133C LEU* 1.3 60.5 + - - +
3134C PRO* 3.5 4.3 - - - +
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Residues in contact with LEU3133 (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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3014C LEU* 4.5 0.9 - - - -
3015C TYR* 2.7 35.0 + - + +
3092C ASN 3.8 16.8 - - - +
3093C HIS* 3.6 27.4 - - + +
3094C TYR* 3.5 29.8 - - + +
3132C PHE* 1.3 72.3 - - - +
3134C PRO* 1.3 67.2 - - + +
3135C LEU* 2.9 48.0 + - + +
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Residues in contact with PRO3134 (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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3012C LYS* 3.8 28.7 - - + +
3013C LEU 3.5 7.0 - - - +
3014C LEU* 4.8 5.4 - - + -
3046C LEU* 6.1 0.2 - - + -
3093C HIS* 3.2 21.8 - - + +
3095C ASN* 3.2 27.8 - - - +
3097C TYR* 4.4 6.1 - - - +
3132C PHE 3.5 5.6 - - - +
3133C LEU* 1.3 88.9 - - + +
3135C LEU* 1.3 64.9 + - - +
3136C PRO* 3.6 10.3 - - + +
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Residues in contact with LEU3135 (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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3012C LYS* 3.7 3.3 - - - +
3013C LEU* 2.9 47.5 + - + +
3015C TYR* 3.7 20.4 - - + +
3022C PHE* 5.2 5.6 - - + -
3133C LEU* 2.9 52.3 - - + +
3134C PRO* 1.3 78.4 - - - +
3136C PRO* 1.3 73.2 - - + +
3137C VAL* 3.3 2.6 + - - +
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Residues in contact with PRO3136 (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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3010C LYS* 5.4 9.9 - - + +
3011C PRO 3.7 9.9 - - - +
3012C LYS* 3.9 14.3 - - + +
3134C PRO* 3.6 10.5 - - + +
3135C LEU* 1.3 86.7 - - + +
3137C VAL* 1.3 65.8 + - - +
3138C SER 4.1 0.3 + - - -
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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