Contacts of the strand formed by residues 3090 - 3095 (chain A) in PDB entry 5NUG
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 VAL3090 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2801A ARG* 4.6 22.7 - - - +
2831A ARG 6.2 0.2 - - - +
2835A ASP* 6.5 0.9 - - + -
2836A ARG* 5.8 0.7 - - - +
2925A ILE* 3.4 37.9 - - + -
2928A GLN* 4.3 17.5 - - - +
2931A GLY* 5.8 0.2 - - - -
2932A HIS 2.8 18.0 + - - +
2933A LEU* 3.7 6.9 - - - +
2934A LEU 3.5 14.4 + - - -
3088A ARG 4.4 5.8 - - - +
3089A CYS* 1.3 70.5 - - - +
3091A LEU* 1.3 62.3 + - - +
3092A ASN* 3.0 10.2 + - + +
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Residues in contact with LEU3091 (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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2791A HIS* 3.7 36.1 - - + +
2835A ASP* 3.8 2.1 - - - +
2836A ARG* 3.7 39.8 + - + +
2934A LEU* 3.8 24.5 - - + +
2936A ILE* 3.7 17.0 - - + -
3075A LEU* 4.9 0.2 - - + -
3085A LEU 4.6 2.0 - - - +
3086A PHE* 3.4 42.0 - - + -
3089A CYS 3.5 6.1 + - - +
3090A VAL* 1.3 72.2 - - - +
3092A ASN* 1.3 76.3 + - - +
3093A TRP* 4.2 5.8 - - + -
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Residues in contact with ASN3092 (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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2835A ASP* 3.7 27.6 - - - +
2918A HIS* 3.4 15.7 + - - -
2921A ARG* 3.8 19.3 + - - +
2922A ILE* 5.3 2.7 - - - -
2925A ILE* 5.6 3.5 - - + +
2933A LEU* 4.4 4.7 - - + -
2934A LEU 2.9 17.5 + - - +
2935A LEU* 3.5 20.6 - - + -
2936A ILE 3.3 6.0 + - - -
3090A VAL* 3.0 11.5 + - + +
3091A LEU* 1.3 84.0 - - - +
3093A TRP* 1.3 73.5 + - - +
3094A PHE* 3.3 31.5 - - - -
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Residues in contact with TRP3093 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2789A GLN* 5.2 4.7 - - - -
2791A HIS* 3.7 34.1 - + - -
2835A ASP 3.5 15.7 + - - +
2836A ARG 4.6 0.7 - - - +
2837A LEU 3.9 13.2 - - - +
2838A VAL* 4.0 37.9 + - + +
2843A ARG* 3.1 27.3 + - - -
2918A HIS* 4.1 3.6 - - - -
2921A ARG* 5.1 0.5 + - - -
2936A ILE* 3.3 41.5 - - + +
3070A PRO* 3.5 26.2 - - + -
3071A SER 5.3 0.4 - - - -
3075A LEU* 3.9 14.8 - - + -
3091A LEU* 4.2 2.9 - - + -
3092A ASN* 1.3 85.4 + - - +
3094A PHE* 1.3 58.3 + - - +
3095A GLY* 3.1 25.3 - - - -
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Residues in contact with PHE3094 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2843A ARG* 5.0 4.2 + - - -
2918A HIS* 3.2 52.2 + + + -
2922A ILE* 4.4 11.0 - - + -
2935A LEU* 3.8 32.8 - - + -
2936A ILE 2.8 6.7 + - - +
2941A ALA* 4.7 9.6 - - + -
2942A GLY 3.7 22.7 - - - -
2943A LYS* 3.7 22.9 - - + -
2946A LEU* 3.8 13.2 - - + -
3092A ASN* 3.3 23.1 - - - -
3093A TRP* 1.3 75.0 - - - +
3095A GLY* 1.3 69.5 + - - +
3096A ASP 3.0 13.5 - - - +
3097A TRP* 5.6 6.7 - + + -
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Residues in contact with GLY3095 (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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2936A ILE 2.8 8.5 + - - -
2937A GLY* 3.1 8.5 - - - -
2938A VAL* 2.8 28.6 + - - -
2941A ALA* 4.1 4.9 - - - +
3070A PRO* 5.0 3.6 - - - -
3093A TRP* 3.1 26.0 - - - -
3094A PHE* 1.3 81.3 - - - +
3096A ASP* 1.3 58.8 + - - -
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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