Contacts of the strand formed by residues 252 - 256 (chain D) in PDB entry 1SID
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 VAL 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D GLN* 3.2 17.5 + - - +
163D HIS* 4.8 3.6 + - - -
244D THR* 6.0 4.7 - - + -
250D PRO* 3.9 7.6 - - + +
251D PRO* 1.3 83.1 - - - +
253D LEU* 1.3 74.0 + - - +
254D GLN* 4.6 4.9 - - - +
286D MET* 4.5 1.9 - - - +
242E ASN* 5.5 0.4 - - - +
243E TYR* 3.0 15.5 - - - +
244E THR* 4.0 16.2 - - + +
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Residues in contact with LEU 253 (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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129D VAL* 3.5 42.0 - - + +
132D SER* 3.7 24.9 - - - +
163D HIS* 4.3 10.1 - - + +
252D VAL* 1.3 80.3 - - - +
254D GLN* 1.3 94.4 + - - +
255D PHE* 5.2 0.7 - - - -
286D MET* 3.5 34.5 - - + -
302D LEU* 4.5 2.5 - - + -
242E ASN* 3.0 8.0 - - - +
243E TYR* 2.9 34.7 + - + -
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Residues in contact with GLN 254 (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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128D GLU* 4.0 12.1 - - - +
129D VAL 5.0 0.7 + - - -
252D VAL* 4.6 4.2 - - - +
253D LEU* 1.3 110.8 + - + +
255D PHE* 1.3 64.1 + - - +
256D THR* 3.1 9.6 + - - +
241E GLY 3.6 3.5 - - - +
242E ASN* 3.0 25.4 + - - +
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Residues in contact with PHE 255 (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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128D GLU* 3.8 12.6 - - - -
129D VAL 3.9 11.9 - - - -
130D VAL* 4.1 15.9 - - + -
131D GLY 4.2 0.2 - - - -
132D SER* 3.0 33.4 - - - -
253D LEU 4.0 0.2 + - - -
254D GLN* 1.3 76.5 - - - +
256D THR* 1.3 68.6 + - - +
162E TYR* 3.3 32.1 - + - -
164E VAL* 3.8 19.7 - - + -
228E HIS* 3.6 21.1 - - - -
229E PRO* 4.3 13.5 - - + -
239E TYR* 4.1 9.2 - - + -
240E PHE* 3.0 16.9 - - - +
241E GLY 2.6 30.8 + - - +
242E ASN* 4.1 4.5 - - - -
243E TYR 5.0 0.2 - - - -
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Residues in contact with THR 256 (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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126D LYS* 5.6 2.3 - - - +
127D THR 4.5 6.9 - - - +
128D GLU* 3.1 27.6 - - - +
254D GLN* 3.1 11.8 + - - +
255D PHE* 1.3 75.0 + - - +
257D ASN* 1.3 62.2 + - - +
258D THR* 2.9 27.5 + - - +
259D LEU* 3.3 27.0 + - + +
239E TYR* 2.5 26.1 + - - -
240E PHE* 3.3 7.6 - - + -
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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