Contacts of the helix formed by residues 360 - 368 (chain a) in PDB entry 5W97
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 360 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306a THR* 3.9 2.8 - - - +
310a MET* 4.0 8.8 - - - +
356a ILE 2.9 28.5 + - - -
357a VAL* 2.9 17.6 + - - +
358a LEU 2.9 2.2 + - - +
359a ALA* 1.3 74.4 - - - +
361a SER* 1.3 61.9 + - - +
362a SER 3.1 0.7 - - - -
363a LEU* 3.1 5.8 + - + +
364a ASP* 2.8 28.9 + - - +
23b PHE* 3.5 23.9 - - + -
27b THR* 4.8 3.0 - - - +
76b ILE* 3.6 19.9 - - - +
80b SER* 2.6 35.4 + - - +
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Residues in contact with SER 361 (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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293a PHE* 3.7 37.6 - - - +
302a ARG* 3.7 7.5 + - - -
306a THR* 2.8 26.5 + - - +
359a ALA 3.2 0.8 + - - -
360a ASN* 1.3 71.4 - - - +
362a SER* 1.3 61.0 + - - +
364a ASP* 4.0 1.0 - - - +
365a ILE* 3.6 24.3 + - - +
80b SER* 4.5 1.1 + - - -
81b LEU* 5.2 0.5 - - - +
84b LEU* 3.0 39.8 - - - +
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Residues in contact with SER 362 (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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360a ASN* 4.8 0.9 - - - -
361a SER* 1.3 82.9 + - - +
363a LEU* 1.3 63.3 + - - +
365a ILE* 3.6 7.8 + - - +
20b LEU* 3.7 19.5 - - - +
23b PHE* 4.9 3.1 - - - -
80b SER* 2.6 39.6 + - - -
83b ILE* 3.4 6.8 - - - +
84b LEU* 3.1 18.5 + - - +
87b MET* 3.4 29.1 - - - +
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Residues in contact with LEU 363 (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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357a VAL* 4.0 29.6 - - + +
360a ASN* 3.1 14.4 + - + +
362a SER* 1.3 76.6 - - - +
364a ASP* 1.3 65.0 + - - +
365a ILE 3.1 2.7 - - - -
366a VAL* 3.2 28.1 - - + +
367a LEU* 3.2 14.8 + - + +
9b PHE* 3.7 33.2 - - + -
20b LEU* 4.2 13.5 - - + +
23b PHE* 3.6 32.5 - - + -
24b HIS* 4.1 20.6 - - + -
27b THR* 4.9 2.9 - - - +
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Residues in contact with ASP 364 (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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290a HIS 4.1 1.9 - - - +
291a HIS 5.8 0.2 - - - -
293a PHE* 3.5 33.9 + - + +
294a THR* 5.0 0.4 - - - -
357a VAL 5.2 0.2 + - - -
358a LEU* 3.6 24.5 - - - +
360a ASN 2.8 16.4 + - - +
361a SER 4.3 2.0 - - - +
362a SER 3.3 0.6 - - - -
363a LEU* 1.3 73.9 - - - +
365a ILE* 1.3 60.5 + - - +
367a LEU* 3.7 7.0 - - - +
368a HIS* 2.6 45.8 + - - +
602a HEA 2.3 39.8 - - - +
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Residues in contact with ILE 365 (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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293a PHE* 3.7 23.8 - - + +
294a THR* 4.3 8.1 - - + -
302a ARG* 5.4 7.4 - - - +
361a SER 3.6 12.1 + - - +
362a SER 3.6 16.4 + - - +
363a LEU 3.1 1.0 - - - -
364a ASP* 1.3 77.2 - - - +
366a VAL* 1.3 59.3 + - + +
87b MET* 4.1 19.7 - - + -
169b GLY 3.5 18.2 - - - +
170b LEU* 4.0 1.1 - - - -
171b LYS* 2.9 74.6 + - - +
23h GLN* 5.9 1.8 - - - +
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Residues in contact with VAL 366 (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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363a LEU* 3.2 21.3 - - + +
365a ILE* 1.3 79.7 - - + +
367a LEU* 1.3 59.9 + - - +
370a THR* 3.5 9.2 - - - +
432a GLY 4.9 2.3 - - - +
435a GLY* 5.9 0.7 - - - -
9b PHE* 3.7 33.3 - - + -
17b MET* 3.9 14.6 - - + -
20b LEU* 4.2 13.0 - - + -
166b PRO* 4.4 14.0 - - + +
169b GLY* 3.6 35.0 - - - +
170b LEU 4.5 2.7 - - - +
171b LYS* 3.1 13.0 + - - +
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Residues in contact with LEU 367 (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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357a VAL* 3.8 26.5 - - + +
358a LEU* 3.7 29.8 - - + -
363a LEU* 3.2 31.1 + - + +
364a ASP* 4.2 2.9 - - - +
366a VAL* 1.3 76.5 - - + +
368a HIS* 1.3 64.8 + - - +
369a ASP 3.4 0.3 + - - -
370a THR* 2.7 25.3 + - - +
372a TYR* 3.9 26.2 - - + -
373a VAL* 3.5 8.1 - - - +
432a GLY 4.8 1.8 - - - +
433a LEU* 4.0 12.3 - - + -
9b PHE* 3.9 26.7 - - + -
24b HIS* 5.7 0.4 - - + -
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Residues in contact with HIS 368 (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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129a TYR* 6.0 1.1 - - - -
291a HIS 4.2 18.9 + - - -
292a MET* 5.9 1.1 - - - -
293a PHE 5.8 0.6 + - - -
294a THR* 3.1 35.9 + - + -
364a ASP* 2.6 29.7 + - - +
366a VAL 3.6 1.0 - - - -
367a LEU* 1.3 72.3 - - - +
369a ASP* 1.3 84.7 + - + +
370a THR 3.2 0.5 + - - -
438a ARG* 5.7 2.7 - - - -
602a HEA 3.0 41.4 + - - +
604a MG 2.0 33.2 - - - -
171b LYS* 2.6 32.1 + - + -
173b ASP* 4.7 1.3 - - - -
197b SER 4.8 0.4 - - - -
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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