Contacts of the strand formed by residues 180 - 185 (chain D) in PDB entry 1SZP
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 ILE 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D SER* 1.3 75.0 - - - +
181D THR* 1.3 68.5 + - - +
182D GLU* 5.2 0.4 - - + -
307D MET* 3.4 46.0 - - + +
310D LEU* 3.9 7.0 - - + -
311D GLN* 3.9 25.2 + - + +
314D ALA* 5.6 0.4 - - + -
321D VAL* 3.5 23.3 - - + +
323D VAL* 4.4 10.8 - - + -
353D SER 3.5 22.2 - - - +
354D SER* 3.7 17.3 - - - -
355D THR* 3.3 24.6 + - - +
356D THR 3.3 5.4 + - - -
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Residues in contact with THR 181 (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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171D LEU* 6.1 0.4 - - + -
175D VAL* 4.5 12.7 - - + +
176D GLU* 4.1 22.2 + - - +
179D SER* 4.1 2.4 + - - -
180D ILE* 1.3 83.3 + - - +
182D GLU* 1.3 60.5 + - - +
183D LEU* 4.0 7.5 + - + -
321D VAL 3.0 9.6 + - - -
322D VAL* 3.3 16.7 - - + +
323D VAL 3.1 23.0 + - - +
356D THR* 3.3 32.4 + - + +
358D LEU* 4.3 18.4 - - + -
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Residues in contact with GLU 182 (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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180D ILE* 4.2 0.6 - - + -
181D THR* 1.3 71.8 - - - +
183D LEU* 1.3 67.1 + - - +
184D PHE* 3.8 10.9 + - + -
323D VAL* 3.3 13.2 - - + +
325D ASN* 3.4 28.6 - - + +
347D GLY 4.5 1.0 - - - +
350D MET* 3.5 26.7 - - + +
351D ALA 4.0 2.4 + - - -
354D SER* 3.6 21.4 + - - +
356D THR 2.8 10.4 + - - +
357D ARG* 3.0 40.6 + - - -
358D LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 183 (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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181D THR* 4.5 7.2 - - + +
182D GLU* 1.3 74.2 - - - +
184D PHE* 1.3 61.9 + - - +
191D LYS* 3.8 15.9 - - + +
194D LEU* 4.3 27.8 - - + -
195D CYS* 4.6 6.7 - - - -
198D LEU* 6.1 0.4 - - + -
322D VAL* 4.2 24.2 - - + -
323D VAL 2.7 13.4 + - - +
324D THR* 2.9 17.9 - - + -
325D ASN 2.7 25.3 + - - -
358D LEU* 3.5 40.2 - - + +
360D PHE* 3.9 12.1 - - + -
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Residues in contact with PHE 184 (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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182D GLU* 4.0 13.2 - - + +
183D LEU* 1.3 76.5 - - - +
185D GLY* 1.3 63.7 + - - +
191D LYS* 3.5 7.2 - - - +
325D ASN* 3.1 25.4 - - + +
327D VAL* 5.0 10.1 - - + -
357D ARG* 3.8 31.2 - - - -
358D LEU 3.1 25.1 + - - +
359D GLY* 3.7 10.8 - - - -
360D PHE* 3.0 21.7 + - - +
373D VAL* 3.6 26.0 - - + -
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Residues in contact with GLY 185 (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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184D PHE* 1.3 82.2 - - - +
186D GLU* 1.3 64.3 + - - -
189D THR* 4.1 1.1 - - - -
191D LYS* 3.1 19.9 + - - +
325D ASN 3.3 3.2 + - - -
326D GLN* 3.5 1.0 - - - -
327D VAL* 3.2 25.0 + - - +
360D PHE 3.8 13.7 - - - -
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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