Contacts of the strand formed by residues 255 - 263 (chain H) in PDB entry 1S9C
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 THR 255 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H THR* 4.2 12.8 - - - -
178H ASP 3.3 18.6 - - - +
179H THR* 4.0 19.4 + - - +
253H GLY 4.4 0.9 + - - -
254H GLN* 1.3 74.3 - - - +
256H LEU* 1.3 69.6 + - - +
273H VAL* 3.3 6.9 - - - -
274H GLN* 2.9 40.3 + - + +
275H GLU* 2.7 25.9 + - - -
171I PRO* 4.4 17.5 - - + +
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Residues in contact with LEU 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H LEU 4.6 0.2 - - - -
177H THR* 3.1 8.0 - - - -
178H ASP* 2.6 42.4 + - + +
180H THR* 4.0 15.3 - - - +
214H LEU* 5.4 1.8 - - + -
219H THR* 3.7 32.3 - - + +
222H PHE* 3.6 45.3 - - + -
223H SER 5.4 0.4 - - - +
250H VAL* 4.0 27.4 - - + -
255H THR* 1.3 77.3 - - - +
257H GLN* 1.3 61.1 + - - +
258H THR* 5.1 3.8 - - - +
271H THR* 4.4 8.3 - - + -
272H LYS 3.4 9.9 - - - +
273H VAL* 4.5 2.5 - - + -
280H VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H VAL* 3.9 17.9 - - + +
176H LEU 3.7 2.2 - - - -
177H THR* 3.8 21.0 - - + +
256H LEU* 1.3 74.7 - - - +
258H THR* 1.3 61.5 + - - +
259H GLU* 3.6 8.9 + - + +
270H GLN 3.6 0.3 - - - +
271H THR* 3.2 3.7 - - - -
272H LYS* 2.8 62.1 + - + +
274H GLN* 2.9 43.2 - - - +
277H GLY* 5.8 1.0 - - - -
171I PRO* 4.9 1.6 - - - +
172I PRO* 5.9 2.2 - - - +
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Residues in contact with THR 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H VAL* 3.2 4.6 - - - -
176H LEU 2.9 35.7 + - - -
178H ASP* 5.0 2.3 + - - -
222H PHE* 5.6 0.5 - - - +
223H SER* 2.8 51.8 + - - +
226H ARG* 4.6 9.0 - - + +
227H VAL* 4.8 0.4 - - + -
256H LEU* 5.1 4.0 - - - +
257H GLN* 1.3 74.0 + - - +
259H GLU* 1.3 60.9 + - - +
260H MET* 3.8 27.1 - - + +
269H PHE* 4.2 9.6 - - + -
270H GLN 3.6 6.5 - - - +
271H THR* 4.0 3.3 - - - +
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Residues in contact with GLU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H PRO* 4.1 17.0 - - + +
174H ALA 3.7 4.5 - - - -
175H VAL* 4.0 15.2 - - + +
257H GLN* 4.2 12.0 - - + +
258H THR* 1.3 75.0 - - - +
260H MET* 1.3 60.1 + - - +
261H TRP* 3.3 19.8 - - + -
269H PHE* 3.0 8.5 - - - +
270H GLN* 2.8 65.5 + - - +
272H LYS* 3.0 37.0 + - + +
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Residues in contact with MET 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H PRO* 3.6 1.6 - - - +
173H ASP* 2.8 33.1 + - - -
174H ALA 2.7 22.6 + - - +
176H LEU* 3.4 41.7 - - + +
226H ARG* 4.4 5.4 - - + -
227H VAL* 3.8 32.3 - - + -
230H GLN* 4.1 7.9 - - + -
231H PHE* 3.5 31.6 - - + -
258H THR* 3.8 24.5 - - + +
259H GLU* 1.3 79.2 - - - +
261H TRP* 1.3 57.8 + - - +
262H LYS 4.3 0.4 - - - -
267H ILE* 4.1 2.9 - - + -
268H HIS 3.3 6.1 - - - +
269H PHE* 4.2 1.8 - - + -
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Residues in contact with TRP 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167H ILE* 3.7 29.2 - - + -
168H PRO* 3.7 42.4 + - + -
170H ARG* 2.7 46.2 + - - +
172H PRO* 3.3 32.9 - - + +
173H ASP* 3.4 4.7 - - - -
231H PHE* 5.2 0.2 - - - -
259H GLU* 3.3 45.1 - - + -
260H MET* 1.3 76.3 - - - +
262H LYS* 1.3 63.2 + - - +
263H GLU 3.6 1.3 + - - -
267H ILE* 3.3 5.2 - - - -
268H HIS* 2.8 53.9 + - + +
269H PHE* 4.1 1.6 - - - -
270H GLN* 3.8 13.5 - - + -
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Residues in contact with LYS 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H ARG* 3.4 14.0 + - - -
173H ASP* 2.8 16.7 + - - +
231H PHE* 3.7 31.8 - - + -
261H TRP* 1.3 73.0 - - - +
263H GLU* 1.3 63.9 + - - +
264H GLY* 3.0 27.0 + - - +
265H ASN* 5.9 0.7 - - - +
267H ILE* 3.5 18.4 - - + -
39I LYS 5.5 4.2 + - - -
40I ASP* 6.3 0.4 - - - +
41I PRO* 5.7 6.5 - - - +
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Residues in contact with GLU 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H PRO* 3.9 15.1 - - + +
170H ARG* 2.7 37.8 + - - +
261H TRP 4.6 0.4 - - - +
262H LYS* 1.3 73.5 - - - +
264H GLY* 1.3 63.0 + - - +
265H ASN 3.3 0.3 + - - -
266H ARG* 3.0 28.8 + - - +
268H HIS* 3.6 29.2 - - + +
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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