Contacts of the strand formed by residues 252 - 261 (chain D) in PDB entry 2WLM
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 GLN 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ALA* 4.7 16.0 + - - +
38C TYR* 4.7 5.4 + - - -
136D THR* 3.6 23.3 + - - +
138D PRO* 2.9 31.1 - - + +
246D HIS* 3.4 12.2 - - - -
247D HIS* 2.9 27.3 + - - +
250D PHE* 3.5 16.0 - - + +
251D ALA* 1.3 79.1 - - - +
253D ASN* 1.3 70.3 + - + +
254D VAL* 4.1 1.1 - - - +
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Residues in contact with ASN 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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246A HIS* 5.3 16.1 - - + +
138D PRO* 4.4 7.3 - - - +
173D GLU* 5.2 5.9 + - - +
244D THR* 5.5 2.8 + - - -
245D GLY* 3.5 20.6 + - - +
246D HIS* 3.4 24.6 + - - +
252D GLN* 1.3 87.9 + - - +
254D VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 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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138D PRO* 3.6 27.1 - - + -
139D THR* 4.2 0.9 - - - +
140D ALA* 3.7 34.8 - - + +
171D ILE* 4.4 7.0 - - + -
243D PHE* 4.7 0.7 - - + -
244D THR* 3.4 2.4 - - - -
245D GLY 2.8 46.6 + - - +
247D HIS* 3.7 32.8 - - + +
250D PHE* 4.1 2.0 - - + -
252D GLN 4.1 0.7 - - - +
253D ASN* 1.3 82.2 - - - +
255D HIS* 1.3 68.6 + - - +
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Residues in contact with HIS 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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172A ILE* 3.0 25.3 - - + +
246A HIS* 3.5 32.0 + + - -
248A GLU* 3.2 38.7 - - + +
251A ALA* 6.0 0.7 - - + -
139D THR* 5.3 1.6 - - - +
140D ALA* 3.9 15.3 + - - +
242D LEU* 4.2 2.7 - - + -
243D PHE* 3.0 17.5 - - - +
244D THR* 3.4 13.2 - - + +
253D ASN 6.0 0.2 - - - -
254D VAL* 1.3 78.5 + - - +
256D ALA* 1.3 68.9 + - - +
257D ARG* 5.5 2.5 - - + -
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Residues in contact with ALA 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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140D ALA* 4.3 14.4 - - + +
142D VAL* 4.4 10.5 - - + +
144D PHE* 3.7 24.7 - - + -
242D LEU* 3.5 3.8 - - - +
243D PHE* 2.7 36.6 + - + +
255D HIS* 1.3 80.5 - - - +
257D ARG* 1.3 62.8 + - - +
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Residues in contact with ARG 257 (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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170A GLN* 2.8 36.6 + - - +
207A ILE* 4.0 23.8 - - + -
248A GLU* 2.8 39.0 + - - +
17D SER 4.4 0.2 - - - +
18D ASP* 3.0 40.1 + - - +
19D GLY* 4.4 6.1 - - - -
20D SER* 3.0 22.2 - - - +
144D PHE* 3.9 8.3 - - - -
241D VAL 3.1 11.0 - - - +
242D LEU* 4.6 4.0 - - + -
255D HIS* 5.5 2.9 - - + -
256D ALA* 1.3 77.6 - - - +
258D HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 258 (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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17D SER* 3.4 26.9 + - - -
18D ASP* 5.5 0.4 - - - -
19D GLY* 4.6 1.1 - - - +
144D PHE* 3.4 40.9 - + + +
145D SER 4.2 3.2 + - - -
146D SER* 4.7 5.9 + - - -
240D LEU* 2.8 7.9 - - - +
241D VAL* 2.7 35.1 + - + +
257D ARG* 1.3 77.7 + - - +
259D ALA* 1.3 72.4 + - - +
260D TYR* 3.2 48.5 + + - -
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Residues in contact with ALA 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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13D ARG* 3.9 12.6 + - - +
15D LEU* 4.4 12.8 - - + -
16D ASN 3.1 27.1 - - - +
17D SER* 3.0 12.4 + - - -
19D GLY* 4.2 1.3 - - - -
238D GLU* 5.5 2.0 - - + +
239D PHE 3.2 8.1 - - - +
240D LEU* 3.8 14.8 - - + -
258D HIS* 1.3 91.3 + - - +
260D TYR* 1.3 65.3 + - - +
264D GLU* 4.5 2.6 - - - +
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Residues in contact with TYR 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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13D ARG* 4.3 3.8 - - - -
144D PHE* 3.8 1.9 - - - +
145D SER* 2.3 41.0 + - - -
146D SER 3.3 19.7 - - - -
147D ARG 3.9 5.4 - - - -
148D MET* 3.3 43.3 - - + -
161D MET* 3.5 16.8 - - + +
238D GLU* 3.3 7.4 - - - +
239D PHE* 2.6 45.9 + - + +
241D VAL* 4.0 21.1 - - + -
258D HIS* 3.2 29.5 - + - -
259D ALA* 1.3 78.7 - - - +
261D SER* 1.3 66.6 + - - +
264D GLU* 4.2 13.2 - - + -
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Residues in contact with SER 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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13D ARG* 4.1 19.8 + - - +
237D SER 4.3 0.2 - - - -
238D GLU* 4.5 14.6 - - - -
239D PHE* 5.0 1.7 - - - -
260D TYR* 1.3 76.8 - - - +
262D CYS* 1.3 73.6 + - - +
263D ASP* 2.7 23.8 + - - -
264D GLU* 2.9 38.7 + - - +
265D ILE* 3.9 6.5 + - - +
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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