Contacts of the strand formed by residues 214 - 220 (chain A) in PDB entry 4WTM
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 PRO 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A TRP* 3.4 62.1 - - + +
211A LYS* 3.8 20.6 - - + +
212A LYS 4.0 2.2 - - - +
213A ASP* 1.3 95.3 - - - +
215A MET* 1.3 59.5 + - - +
323A ILE* 4.7 0.9 - - + -
324A SER 3.3 8.1 - - - +
326A SER* 4.5 0.2 - - - -
358A TYR* 3.5 22.5 - - - +
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Residues in contact with MET 215 (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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208A TRP* 4.3 5.2 - - - -
214A PRO* 1.3 74.5 - - - +
216A GLY* 1.3 85.7 + - - +
217A PHE* 4.0 12.8 - - + -
308A ILE* 4.4 8.3 - - + -
322A VAL 3.9 0.2 - - - +
323A ILE* 3.4 2.8 - - - +
324A SER* 2.8 50.5 + - - +
325A GLU 5.4 1.1 - - - +
326A SER* 4.1 9.2 - - - +
332A ASP* 3.8 26.7 - - + +
336A LEU* 3.8 21.3 - - + -
356A PRO* 3.9 17.5 - - + -
357A GLU 3.4 9.4 - - - +
358A TYR* 3.7 23.3 - - + -
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Residues in contact with GLY 216 (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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208A TRP* 4.0 6.5 - - - -
215A MET* 1.3 80.5 - - - +
217A PHE* 1.3 61.4 + - - +
322A VAL 3.2 10.8 - - - -
323A ILE* 4.3 1.8 - - - -
357A GLU* 2.8 38.5 + - - +
363A ILE* 3.5 20.0 - - - -
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Residues in contact with PHE 217 (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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215A MET* 4.0 10.1 - - + -
216A GLY* 1.3 74.6 - - - +
218A SER* 1.3 72.6 + - - +
219A TYR* 4.6 1.8 - - + -
308A ILE* 4.2 13.5 - - + -
320A LEU* 4.6 4.9 - - + -
321A ILE* 3.4 5.0 - - - +
322A VAL* 3.0 69.1 + - + -
336A LEU* 3.8 32.5 - - + -
339A PHE* 3.9 45.5 - + - -
354A PRO* 4.2 8.3 - - + -
355A ARG 3.4 20.6 - - - +
356A PRO* 4.5 0.2 - - + -
357A GLU* 5.5 0.2 - - - -
363A ILE* 3.9 11.3 - - - +
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Residues in contact with SER 218 (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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217A PHE* 1.3 79.0 - - - +
219A TYR* 1.3 61.9 + - - +
320A LEU 3.1 11.7 - - - -
321A ILE* 4.4 0.2 - - - -
354A PRO* 3.4 24.6 - - - +
355A ARG 5.0 1.2 + - - +
363A ILE* 4.1 12.3 - - - +
364A THR 3.0 31.8 + - - -
365A SER* 4.4 4.9 - - - -
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Residues in contact with TYR 219 (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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217A PHE* 4.6 1.8 - - + -
218A SER* 1.3 76.6 - - - +
220A ASP* 1.3 81.0 + - - +
221A THR* 3.7 11.7 - - - -
318A ASP 3.6 1.7 - - - +
319A ASP* 3.6 1.9 - - - +
320A LEU* 2.9 54.9 + - + +
339A PHE* 3.7 22.2 - + + -
340A THR* 4.1 9.9 - - + +
343A MET* 3.5 33.8 - - + +
348A ALA 2.7 29.2 + - - -
350A PRO* 3.0 36.6 - - + +
352A ASP 5.4 1.6 - - - -
354A PRO* 3.8 26.7 - - + -
365A SER* 4.9 0.7 + - - -
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Residues in contact with ASP 220 (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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219A TYR* 1.3 82.3 - - - +
221A THR* 1.3 61.4 + - - +
318A ASP* 2.9 7.1 - - - +
319A ASP* 2.4 18.0 - - - +
350A PRO* 3.5 7.1 - - - +
351A GLY* 3.2 21.8 + - - -
352A ASP 4.9 2.7 + - - +
601A MN 2.0 31.6 + - - -
602A MN 2.1 31.7 + - - -
605A UDP 3.2 0.2 + - - -
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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