Contacts of the strand formed by residues 256 - 264 (chain D) in PDB entry 1ML3
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 SER 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C ILE* 4.9 1.8 - - - -
192D THR* 4.2 0.7 - - - -
193D ILE 3.4 13.2 - - - -
194D HIS* 3.3 12.1 - - - -
195D SER 3.1 21.5 + - - -
255D VAL* 1.3 73.8 - - - +
257D VAL* 1.3 63.3 + - - +
332D TRP* 3.5 9.4 - - - -
333D TYR* 2.9 58.4 + - - -
335D ASN* 3.2 10.8 + - - -
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ILE* 4.6 2.7 - - + -
248C PHE* 4.1 17.9 - - + -
191D THR 3.7 0.3 - - - +
192D THR* 3.2 4.9 - - - -
193D ILE* 3.1 53.4 + - + +
256D SER* 1.3 80.5 - - - +
258D VAL* 1.3 76.1 + - - +
330D VAL* 3.7 22.4 - - + -
331D SER 3.3 15.0 - - - +
332D TRP* 3.8 23.6 - - + -
333D TYR* 4.0 1.8 - - - -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D THR* 4.0 24.9 - - + +
170D CYS* 3.6 26.7 - - + -
171D LEU* 4.5 13.0 - - + +
174D ILE* 6.2 2.2 - - + -
190D MET* 4.1 19.7 - - + -
191D THR 3.7 2.7 - - - -
192D THR* 4.5 1.8 - - - -
257D VAL* 1.3 75.3 - - - +
259D ASP* 1.3 62.3 + - - +
260D LEU* 4.0 19.5 - - + +
329D ILE 3.5 1.8 - - - +
330D VAL* 3.4 5.0 - - - -
331D SER* 2.7 42.4 + - - +
333D TYR* 3.9 11.9 - - + -
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Residues in contact with ASP 259 (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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191C THR* 2.5 36.3 + - - +
248C PHE* 4.5 12.1 - - + -
259C ASP* 4.9 1.7 - - - +
189D LEU 4.0 0.2 - - - +
190D MET* 3.4 2.4 - - - -
191D THR* 2.7 44.7 + - - +
193D ILE* 4.5 13.0 - - + -
258D VAL* 1.3 75.0 - - - +
260D LEU* 1.3 59.0 + - - +
261D THR* 3.8 4.0 + - - -
328D LYS* 2.8 34.7 + - - +
329D ILE 3.8 2.5 - - - -
330D VAL* 4.3 2.9 - - - +
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Residues in contact with LEU 260 (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* 4.1 21.5 - - + -
174D ILE* 4.3 19.1 - - + -
175D VAL* 4.5 8.1 - - + -
178D LEU* 4.5 5.2 - - + -
185D VAL* 6.1 2.5 - - + -
188D GLY* 4.6 3.6 - - - -
189D LEU 3.5 19.7 - - - +
190D MET* 4.0 9.4 - - + -
243D LEU* 5.2 9.0 - - + -
258D VAL* 3.8 12.8 - - + -
259D ASP* 1.3 73.9 + - - +
261D THR* 1.3 77.7 + - - +
262D PHE* 4.2 22.0 - - + -
327D PHE 3.6 1.2 - - - +
328D LYS* 3.2 4.2 - - - -
329D ILE* 2.8 48.5 + - + +
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Residues in contact with THR 261 (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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189C LEU* 4.1 8.6 + - + +
261C THR* 3.6 39.5 + - + -
326C PHE* 3.5 2.5 - - + -
188D GLY* 3.3 0.5 - - - -
189D LEU 2.8 39.3 + - - +
259D ASP* 4.5 3.8 + - - -
260D LEU* 1.3 76.6 - - - +
262D PHE* 1.3 66.1 + - - +
326D PHE* 3.7 25.4 - - + -
327D PHE 3.2 10.1 - - - +
328D LYS* 4.3 15.6 + - - +
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Residues in contact with PHE 262 (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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326C PHE* 3.8 6.3 - - - -
178D LEU* 3.7 23.1 - - + -
184D GLY 4.0 11.4 - - - -
185D VAL* 4.3 13.7 - - + -
187D THR 3.4 14.4 - - - +
188D GLY* 3.9 5.2 - - - -
260D LEU* 4.2 18.8 - - + -
261D THR* 1.3 80.3 - - - +
263D THR* 1.3 73.0 + - - +
264D ALA* 3.9 22.0 - - + -
273D ILE* 3.9 20.2 - - + -
325D ARG 3.1 1.9 - - - +
326D PHE* 3.4 2.1 - - - -
327D PHE* 2.7 59.9 + + + -
329D ILE* 3.2 30.5 - - + -
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Residues in contact with THR 263 (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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263C THR* 4.6 5.8 - - + -
326C PHE* 4.1 9.4 - - + -
186D GLN* 3.1 32.1 + - - +
187D THR* 3.0 27.9 + - - +
262D PHE* 1.3 79.6 - - - +
264D ALA* 1.3 67.7 + - - +
325D ARG* 2.9 15.5 - - + +
326D PHE* 3.6 31.6 - - + +
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Residues in contact with ALA 264 (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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183D PHE* 3.9 9.4 - - + +
184D GLY 3.3 13.2 - - - +
186D GLN* 4.2 6.7 - - - +
262D PHE* 3.8 12.9 - - + -
263D THR* 1.3 78.8 - - - +
265D ALA* 1.3 62.7 + - - +
266D ARG 3.2 22.2 - - - +
268D THR* 3.8 14.1 - - - +
273D ILE* 5.7 0.7 - - + -
325D ARG* 2.8 30.5 + - - +
327D PHE* 4.4 3.8 - - + -
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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