Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 5WWT
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 ASN 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PRO* 4.8 0.9 - - - +
54A THR* 3.5 4.7 - - - -
126A ARG* 2.4 29.0 + - - +
219A GLN* 1.3 73.9 - - - +
221A LEU* 1.3 67.2 + - - +
222A PRO* 3.4 5.2 - - + -
223A SER* 3.0 14.4 + - - +
224A ALA* 3.1 11.1 + - - +
456A ILE* 3.4 37.8 - - + +
72C C 3.5 13.5 + - - -
73C U 2.7 47.1 + - - +
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Residues in contact with LEU 221 (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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54A THR* 3.4 17.3 + - + +
89A HIS* 3.9 13.9 - - + +
92A LEU* 3.6 25.3 - - + +
95A VAL* 3.9 22.0 - - + -
97A LEU* 4.0 11.2 - - + -
219A GLN 4.5 0.4 - - - -
220A ASN* 1.3 69.6 - - - +
222A PRO* 1.3 66.8 - - + +
224A ALA* 3.3 7.5 + - - +
225A LEU* 2.9 26.8 + - + +
403A ILE* 4.5 9.4 - - + -
424A PHE* 5.1 4.3 - - + -
451A ALA* 3.4 27.8 - - + +
452A ASN* 3.4 26.0 - - - +
455A SER* 5.2 4.7 - - - -
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Residues in contact with PRO 222 (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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220A ASN* 3.5 4.9 - - + -
221A LEU* 1.3 95.1 - - + +
223A SER* 1.3 57.3 + - - +
225A LEU* 3.0 10.8 + - + +
226A VAL* 2.9 33.8 + - - +
424A PHE* 3.5 30.1 - - + -
455A SER* 4.5 12.6 - - - +
456A ILE* 3.9 17.0 - - + +
458A PHE* 3.5 38.8 - - + -
460A ILE* 4.0 1.0 - - - +
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Residues in contact with SER 223 (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 GLN* 3.3 21.0 + - - -
220A ASN* 3.0 10.1 + - - +
222A PRO* 1.3 80.4 - - - +
224A ALA* 1.3 61.1 + - - +
226A VAL* 3.5 15.2 + - - +
227A SER* 4.2 2.6 + - - -
248A LYS* 3.7 24.2 - - - +
456A ILE* 4.7 0.2 - - - +
458A PHE* 3.5 7.9 - - - -
72C C 3.2 19.1 + - - +
73C U 2.9 28.6 + - - -
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Residues in contact with ALA 224 (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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56A ARG* 4.6 3.6 - - + -
92A LEU* 4.9 1.3 - - + -
95A VAL* 3.9 26.9 - - + -
219A GLN* 3.7 23.2 - - + +
220A ASN 3.1 11.4 + - - +
221A LEU* 3.7 9.0 - - - +
223A SER* 1.3 74.7 - - - +
225A LEU* 1.3 65.3 + - - +
226A VAL 3.4 0.2 + - - -
227A SER 3.6 2.8 + - - -
228A HIS* 3.2 7.2 - - - -
251A HIS* 3.0 32.6 + - + -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.7 23.3 - - + +
221A LEU* 2.9 14.8 + - + +
222A PRO* 3.2 9.9 - - + +
224A ALA* 1.3 76.6 - - - +
226A VAL* 1.3 64.5 + - - +
228A HIS* 3.0 4.9 + - - +
229A VAL* 2.9 25.5 + - + +
401A PRO* 3.6 37.7 - - + +
403A ILE* 3.8 12.3 - - + -
422A GLN* 3.6 19.1 - - - +
424A PHE* 3.5 30.7 - - + -
460A ILE* 3.8 14.4 - - + -
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Residues in contact with VAL 226 (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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222A PRO 2.9 21.0 + - - +
223A SER 3.6 11.0 - - - +
224A ALA 3.2 0.6 - - - -
225A LEU* 1.3 75.6 - - - +
227A SER* 1.3 58.9 + - - +
229A VAL* 3.1 6.5 + - - +
230A LEU* 2.9 27.6 + - + +
248A LYS* 4.0 13.2 - - + -
321A LEU* 3.5 33.9 - - + -
369A VAL* 4.0 11.5 - - + +
371A SER* 4.0 6.7 - - - +
458A PHE* 3.5 28.9 - - + -
460A ILE* 3.7 14.6 - - + -
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Residues in contact with SER 227 (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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223A SER 4.2 3.0 + - - -
224A ALA 3.6 0.8 + - - -
225A LEU 3.3 0.4 - - - -
226A VAL* 1.3 78.8 - - - +
228A HIS* 1.3 61.0 + - - +
230A LEU* 3.6 7.5 + - - +
231A ASN 3.2 15.2 + - - -
232A PRO* 3.3 14.7 - - - +
248A LYS* 3.5 19.8 + - - +
251A HIS* 3.1 44.0 + - - +
252A ILE* 4.0 15.2 - - - +
255A LEU* 3.4 9.5 - - - +
321A LEU* 5.7 0.4 - - - -
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Residues in contact with HIS 228 (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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91A ASP 5.2 0.6 + - - -
92A LEU* 3.9 19.6 - - + +
93A GLN* 3.4 28.8 + - + -
94A ASP* 2.9 38.8 + - - -
224A ALA* 3.2 24.2 - - + -
225A LEU 3.0 8.2 + - - +
227A SER* 1.3 75.7 - - - +
229A VAL* 1.3 63.3 + - - +
231A ASN* 3.1 19.2 + - - +
251A HIS* 3.4 9.7 + + - -
255A LEU* 4.1 19.3 - - + +
400A GLU 3.6 8.4 - - - +
401A PRO* 3.9 17.6 - - + +
65B GLN* 3.7 3.5 - - - +
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Residues in contact with VAL 229 (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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225A LEU* 2.9 34.8 + - + +
226A VAL* 3.5 9.9 - - - +
228A HIS* 1.3 75.2 - - - +
230A LEU* 1.3 65.1 + - - +
231A ASN* 3.3 4.0 + - - +
369A VAL* 4.5 6.5 - - + -
399A GLN* 3.5 34.1 - - + +
400A GLU 3.6 14.0 + - - +
401A PRO 4.3 0.4 - - - +
422A GLN* 3.8 22.4 - - - +
460A ILE* 4.2 11.7 - - + -
462A LYS* 3.6 27.8 - - + -
65B GLN* 4.8 2.3 + - - -
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Residues in contact with LEU 230 (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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226A VAL 2.9 15.6 + - - +
227A SER* 3.7 6.7 - - - +
229A VAL* 1.3 76.5 - - - +
231A ASN* 1.3 61.2 + - - +
232A PRO* 4.6 4.0 - - + -
238A ILE* 3.9 17.7 - - + -
252A ILE* 3.6 34.1 - - + -
319A ARG* 2.8 53.4 + - + -
320A ILE 4.3 5.2 - - - +
321A LEU* 4.0 16.2 - - + +
367A VAL* 4.1 16.4 - - + +
369A VAL* 3.7 29.3 - - + +
462A LYS* 5.1 0.7 - - - -
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Residues in contact with ASN 231 (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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227A SER 3.2 0.6 + - - -
228A HIS 3.1 17.9 + - - +
229A VAL 3.8 4.3 - - - +
230A LEU* 1.3 77.4 - - - +
232A PRO* 1.3 72.1 - - - +
233A GLN* 3.3 9.5 + - - +
255A LEU* 5.7 0.2 - - - -
319A ARG* 3.0 27.7 + - - +
462A LYS* 5.8 1.6 - - - -
63B SER* 2.7 36.5 + - - -
65B GLN* 3.5 38.7 - - - +
66B HIS* 3.8 7.5 + - - +
69B ASN* 5.5 0.8 - - - +
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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