Contacts of the strand formed by residues 3163 - 3168 (chain D) in PDB entry 1W21
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 ALA3163 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108B LYS 5.5 1.8 - - - +
1110B ASN* 5.8 3.1 - - - +
3140D LEU* 3.4 4.2 - - - -
3141D SER* 2.9 33.8 + - - +
3161D PHE 4.3 0.9 + - - +
3162D ARG* 1.3 79.9 - - - +
3164D LEU* 1.3 63.3 + - - +
3165D ILE* 3.5 5.9 + - + +
3180D VAL* 4.1 11.2 - - + -
3182D CYS 3.3 14.8 - - - +
3183D ILE* 3.8 17.3 - - + -
3184D GLY 3.3 8.9 + - - +
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Residues in contact with LEU3164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3127D TYR* 3.4 31.4 - - + +
3138D PHE* 4.0 9.0 - - + -
3139D ALA 3.5 23.1 - - - +
3140D LEU* 4.0 5.6 - - + +
3163D ALA* 1.3 72.6 - - - +
3165D ILE* 1.3 55.8 + - - +
3180D VAL* 3.6 3.8 - - - +
3181D GLU* 2.8 55.4 + - + -
3182D CYS* 2.9 18.6 + - - +
3184D GLY 4.4 0.2 + - - -
3187D SER* 3.3 28.3 - - - +
3188D THR 4.2 8.1 - - - +
3189D SER* 4.5 0.4 - - - -
3198D SER* 4.3 5.4 - - - +
3200D CYS* 3.5 18.6 - - - -
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Residues in contact with ILE3165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121D LEU* 4.0 23.3 - - + -
3123D THR* 4.0 22.7 - - + -
3138D PHE* 3.2 5.2 - - - +
3139D ALA 2.9 37.4 + - - +
3141D SER* 4.0 20.4 - - - +
3163D ALA* 4.4 3.6 - - + +
3164D LEU* 1.3 77.9 - - - +
3166D SER* 1.3 60.6 + - - +
3167D TRP* 3.6 20.0 - - + -
3173D PRO* 4.1 1.8 - - + -
3178D THR* 4.0 22.7 - - + +
3179D ARG 3.1 11.9 - - - +
3180D VAL* 4.2 17.0 - - + -
3181D GLU* 4.4 3.6 - - - -
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Residues in contact with SER3166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3136D ARG* 2.9 27.4 + - - -
3137D MET 3.1 12.6 - - - -
3138D PHE* 3.6 22.4 - - - -
3165D ILE* 1.3 74.1 - - - +
3167D TRP* 1.3 66.8 + - - +
3178D THR* 3.5 1.0 - - - -
3179D ARG* 2.8 35.6 + - - +
3181D GLU* 2.6 28.9 + - - -
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Residues in contact with TRP3167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3109D ASP* 4.2 1.3 - - - -
3123D THR* 5.0 0.7 - - + -
3136D ARG* 3.4 16.3 - - - +
3137D MET* 2.9 51.5 + - + +
3138D PHE 3.7 13.9 - - - -
3139D ALA* 3.7 19.5 - - + -
3165D ILE* 3.6 31.2 - - + -
3166D SER* 1.3 84.9 - - - +
3168D GLU* 1.3 84.5 + - - +
3169D MET 3.3 0.3 + - - -
3171D GLN* 2.8 36.9 + - + -
3172D ALA 4.3 1.3 - - - -
3173D PRO* 3.7 29.5 - - + -
3177D ASN* 3.4 26.5 - - - +
3178D THR* 3.9 18.2 - - + -
3451D ILE* 3.8 15.5 - - + -
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Residues in contact with GLU3168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2179C ARG* 3.6 36.9 + - - +
2180C VAL 4.6 1.7 + - - -
3135D CYS 5.5 1.3 - - - +
3136D ARG* 3.7 17.2 - - + +
3167D TRP* 1.3 83.2 - - - +
3169D MET* 1.3 74.3 + - + +
3170D GLY 3.3 0.5 + - - -
3171D GLN* 3.2 48.5 + - - +
3177D ASN 4.8 1.0 + - - -
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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