Contacts of the strand formed by residues 255 - 263 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171J PRO* 4.4 14.4 - - + +
177K THR* 4.4 5.6 - - - -
178K ASP 3.3 20.4 - - - +
179K THR* 4.0 19.7 + - - +
253K GLY 4.4 1.2 + - - -
254K GLN* 1.3 74.6 + - - +
256K LEU* 1.3 68.1 + - - +
273K VAL* 3.3 5.4 - - - -
274K GLN* 2.9 48.4 + - + +
275K GLU* 2.7 26.1 + - - -
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Residues in contact with LEU 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K THR* 3.3 7.8 - - - -
178K ASP* 2.7 40.9 + - + +
180K THR* 3.9 15.9 - - - +
214K LEU* 5.3 1.8 - - + -
219K THR* 3.7 31.2 - - + +
222K PHE* 3.6 45.3 - - + -
223K SER* 5.5 0.2 - - - +
250K VAL* 4.0 27.8 - - + -
254K GLN 5.5 0.2 - - - +
255K THR* 1.3 78.5 - - - +
257K GLN* 1.3 60.7 + - - +
258K THR* 4.1 4.7 - - - +
271K THR* 4.4 7.9 - - + -
272K LYS 3.4 10.3 - - - +
273K VAL* 4.5 2.2 - - + -
280K VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J PRO* 5.1 1.4 - - - +
172J PRO* 6.0 1.8 - - - +
175K VAL* 4.1 16.1 - - + +
176K LEU 3.9 2.2 - - - -
177K THR* 4.0 20.0 - - + +
256K LEU* 1.3 74.8 - - - +
258K THR* 1.3 62.2 + - - +
259K GLU* 3.6 8.8 + - + +
270K GLN 3.6 1.4 - - - +
271K THR* 3.2 4.3 - - - +
272K LYS* 2.8 62.1 + - + +
274K GLN* 2.9 43.4 - - + +
277K GLY* 5.7 1.0 - - - -
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Residues in contact with THR 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K VAL* 3.2 4.9 - - - -
176K LEU 3.0 35.4 + - - -
178K ASP* 5.1 1.9 + - - -
222K PHE* 5.0 1.0 - - - +
223K SER* 2.7 51.9 + - - +
226K ARG* 4.7 8.7 - - + +
227K VAL* 4.8 0.2 - - + -
256K LEU* 5.0 4.0 - - - +
257K GLN* 1.3 73.4 + - - +
259K GLU* 1.3 61.5 + - - +
260K MET* 3.9 27.1 - - + +
269K PHE* 4.2 12.8 - - + -
270K GLN 3.6 3.4 - - - +
271K THR* 4.0 2.3 - - - +
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Residues in contact with GLU 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PRO* 4.2 14.7 - - + +
174K ALA 3.8 3.8 - - - -
175K VAL* 4.0 15.0 - - + +
257K GLN* 4.2 12.6 - - + +
258K THR* 1.3 74.8 - - - +
260K MET* 1.3 61.0 + - - +
261K TRP* 3.4 20.4 - - + -
269K PHE* 3.0 8.5 - - - +
270K GLN* 2.7 66.3 + - - +
272K LYS* 3.1 35.7 + - + +
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Residues in contact with MET 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PRO* 3.6 2.8 - - - +
173K ASP* 2.8 32.0 + - - -
174K ALA 2.8 22.6 + - - +
176K LEU* 3.5 41.7 - - + +
226K ARG* 4.3 4.9 - - + -
227K VAL* 3.7 28.0 - - + -
230K GLN* 4.2 7.4 - - + -
231K PHE* 3.5 31.4 - - + -
258K THR* 3.9 25.6 - - + +
259K GLU* 1.3 79.4 - - - +
261K TRP* 1.3 58.3 + - - +
267K ILE* 4.1 2.7 - - + -
268K HIS 3.3 6.3 - - - +
269K PHE* 4.2 7.0 - - + -
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Residues in contact with TRP 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ILE* 3.4 31.6 - - + -
168K PRO* 3.7 43.3 + - + -
170K ARG* 2.6 41.0 + - - +
171K PRO 3.8 4.9 - - - -
172K PRO* 3.3 32.0 - - + +
173K ASP* 3.5 4.9 - - - -
259K GLU* 3.4 42.8 - - + -
260K MET* 1.3 77.4 - - - +
262K LYS* 1.3 62.2 + - - +
263K GLU* 3.6 1.3 + - - -
267K ILE* 3.4 6.6 - - - -
268K HIS* 2.8 53.3 + - + +
269K PHE* 4.1 0.9 - - - -
270K GLN* 3.8 15.3 - - + -
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Residues in contact with LYS 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J LYS* 5.4 7.2 + - - -
40J ASP* 6.3 0.6 - - - +
41J PRO* 5.7 6.1 - - - +
170K ARG* 3.3 15.6 + - - -
173K ASP* 2.7 17.8 + - - +
231K PHE* 3.7 30.7 - - + -
261K TRP* 1.3 71.8 - - - +
263K GLU* 1.3 61.9 + - - +
264K GLY* 3.0 27.4 + - - +
265K ASN* 5.9 0.4 - - - +
267K ILE* 3.5 20.2 - - + -
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Residues in contact with GLU 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K PRO* 3.7 15.5 - - + +
170K ARG* 2.8 37.7 + - - +
261K TRP 3.6 0.4 + - - +
262K LYS* 1.3 73.7 - - - +
264K GLY* 1.3 62.8 + - - +
265K ASN 3.3 3.5 + - - -
266K ARG* 3.0 25.7 + - + +
268K HIS* 3.5 30.1 - - + +
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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