Contacts of the strand formed by residues 3194 - 3196 (chain D) in PDB entry 1Y1S
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 ASN3194 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3095D THR* 2.7 32.8 + - - +
3096D GLY 3.2 16.2 - - - +
3097D ALA* 4.1 0.2 - - - -
3098D ILE* 4.2 5.2 - - - -
3108D LEU* 3.4 24.9 - - + +
3110D THR* 5.0 1.0 + - - -
3156D THR* 2.6 35.6 + - - +
3157D ALA* 2.9 30.8 + - - +
3192D VAL* 3.8 3.5 - - - +
3193D MET* 1.3 89.6 - - - +
3195D TYR* 1.3 63.6 + - - +
3196D GLU* 4.7 2.2 - - - +
3215D MET* 5.3 1.0 - - - +
3217D ALA* 4.8 3.4 - - - +
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Residues in contact with TYR3195 (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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3095D THR* 2.4 24.2 + - - -
3096D GLY 2.9 16.4 + - - +
3098D ILE* 3.6 22.4 - - + -
3116D LEU* 4.6 3.1 - - + -
3157D ALA* 3.4 29.8 - - + -
3159D SER* 4.8 3.4 - - - -
3165D GLY 4.0 14.9 + - - -
3166D GLN* 3.0 54.8 - - + +
3183D SER* 4.2 2.1 + - - -
3184D MET* 3.3 36.7 + - + +
3187D TRP* 3.1 30.6 + + + -
3194D ASN* 1.3 75.4 - - - +
3196D GLU* 1.3 58.0 + - - +
3223D ARG* 3.9 8.3 - - + -
8003D URA 3.7 6.8 - - - +
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Residues in contact with GLU3196 (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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3091D ARG* 2.9 40.2 + - - +
3094D THR 4.3 7.0 - - - +
3095D THR* 3.9 13.5 - - - +
3156D THR* 3.4 23.6 - - + -
3157D ALA 3.2 2.8 + - - -
3158D SER* 2.6 17.2 + - - -
3159D SER* 2.9 24.4 + - - -
3166D GLN* 4.3 0.2 + - - -
3194D ASN* 4.8 0.2 - - - +
3195D TYR* 1.3 75.0 - - - +
3197D MET* 1.3 72.5 + - - +
3198D GLU 2.8 5.7 + - - -
3199D SER* 2.3 41.3 + - - +
3215D MET* 3.8 11.2 - - + -
8003D URA 3.4 10.3 + - - -
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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
------------------------------------------------------------
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