Contacts of the strand formed by residues 249 - 255 (chain A) in PDB entry 2W5X
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 PHE 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASN* 2.9 40.5 + - + -
37A VAL 3.0 26.8 + - - -
38A ILE* 3.8 26.0 - - + -
123A ILE* 3.7 5.6 - - - -
124A LYS 3.1 10.5 - - - +
239A ILE* 3.9 12.3 - - + -
242A LEU* 3.6 24.0 - - + +
243A SER* 3.9 31.9 - - - -
247A SER 4.4 0.4 - - - -
248A ALA* 1.3 76.7 - - - +
250A PHE* 1.3 61.1 + - - +
251A ILE* 3.7 22.7 - - + -
287A PHE* 3.6 31.6 - + - -
373A TRP* 4.2 2.6 - - - -
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.3 32.8 - - + -
39A LEU* 4.3 13.5 - - + -
114A ILE* 3.7 35.4 - - + -
115A VAL* 4.3 17.7 - - + -
118A ALA* 4.6 2.0 - - + -
123A ILE* 3.7 3.8 - - + +
124A LYS 2.8 8.4 + - - +
125A THR* 3.3 12.3 - - + -
126A GLY 3.0 25.5 + - - -
127A VAL* 5.9 0.4 - - + -
141A PHE* 3.9 22.9 - + - -
242A LEU* 4.1 0.3 - - - +
249A PHE* 1.3 74.5 - - - +
251A ILE* 1.3 83.2 + - - +
252A MET* 4.1 4.7 - - + -
367A ILE* 4.7 8.3 - - + -
373A TRP* 3.9 24.9 - + + -
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL 3.0 10.4 + - - +
38A ILE* 4.5 13.0 - - + -
39A LEU* 2.8 28.9 + - - +
126A GLY* 3.4 8.7 - - - +
128A VAL* 5.1 1.8 - - + -
235A THR* 4.4 3.8 - - + +
238A ALA* 3.6 16.2 - - + -
239A ILE* 3.6 45.5 - - + +
242A LEU* 3.5 21.3 - - + -
249A PHE* 3.7 17.7 - - + -
250A PHE* 1.3 78.4 - - - +
252A MET* 1.3 64.8 + - - +
253A SER* 3.6 23.8 - - - +
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.1 13.2 - - + +
41A ILE* 3.7 27.6 - - + -
126A GLY 3.0 10.0 + - - +
127A VAL* 3.4 14.0 - - + -
128A VAL 2.8 24.7 + - - +
137A THR* 4.1 7.9 - - + -
138A PRO* 3.7 33.7 - - + -
141A PHE* 3.8 29.2 - - + -
250A PHE* 4.1 15.1 - - + -
251A ILE* 1.3 75.0 - - - +
253A SER* 1.3 78.0 + - - +
254A GLU* 3.9 11.0 - - + -
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 3.0 6.7 + - - -
40A LEU* 3.3 25.1 - - - +
41A ILE 2.9 23.7 + - - -
128A VAL* 3.3 20.3 - - - +
231A LEU* 4.3 7.9 - - - -
235A THR* 3.0 25.2 + - - +
251A ILE* 3.6 16.9 - - - +
252A MET* 1.3 73.6 - - - +
254A GLU* 1.3 61.2 + - - +
255A GLY 4.1 0.2 + - - -
277A PHE* 4.4 1.3 - - - -
280A ALA* 5.9 0.4 - - - -
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.2 16.8 - - + +
43A ASP* 3.0 14.4 - - - +
128A VAL 2.8 15.2 + - - +
129A ALA* 3.8 3.0 - - + +
130A THR* 3.5 12.1 + - - +
131A SER* 4.0 1.2 + - - -
137A THR* 3.0 26.3 + - + +
138A PRO* 3.6 11.4 - - - +
231A LEU* 3.7 13.9 - - - +
252A MET* 4.0 12.1 - - + -
253A SER* 1.3 76.2 - - - +
255A GLY* 1.3 60.1 + - - +
256A SER* 2.7 37.4 + - - +
1379A MG 2.1 30.9 - - - -
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE 2.8 10.3 + - - -
43A ASP 3.1 22.7 + - - -
130A THR* 4.5 2.2 - - - -
227A ARG* 6.2 0.7 - - - -
231A LEU* 4.1 9.6 - - - -
254A GLU* 1.3 68.7 - - - +
256A SER* 1.3 61.3 + - - -
257A GLN 3.4 2.7 + - - -
258A ILE* 3.7 15.8 - - - +
273A GLU 5.7 1.3 - - - -
277A PHE* 3.7 27.3 - - - -
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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