Contacts of the helix formed by residues 333 - 341 (chain C) in PDB entry 3SWD
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 MET 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C THR* 3.5 46.7 - - + +
117C ILE* 5.6 2.5 - - + -
330C ASN 4.7 4.7 + - - +
331C ARG 3.9 1.4 - - - -
332C PHE* 1.3 75.5 - - - +
334C HIS* 1.3 57.1 + - - +
336C PRO* 2.9 22.0 - - - +
337C GLU* 3.7 14.5 - - + +
368C THR* 3.9 36.6 - - + +
369C ASP* 6.3 1.1 - - + -
114D GLY* 4.5 13.0 - - - +
115D QPA 4.0 31.6 - - - +
116D THR* 4.5 9.2 - - + -
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Residues in contact with HIS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C GLN* 3.0 31.5 + - - -
308C ALA* 3.5 31.8 - - + +
311C THR* 3.6 14.3 + - + -
331C ARG* 3.2 22.2 + - + -
332C PHE* 3.9 8.4 - + - -
333C MET* 1.3 73.4 + - - +
335C VAL* 1.3 82.3 + - + +
337C GLU* 3.1 11.2 + - - +
338C LEU* 2.9 29.2 + - + +
368C THR* 5.7 0.2 + - - -
372C ALA* 4.1 15.9 - - + +
373C SER* 5.8 1.8 - - - +
375C SER* 4.0 15.9 - - - +
376C LEU* 4.6 10.3 - - + -
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C THR* 4.2 8.3 - - + -
315C LEU* 5.6 1.7 - - + +
332C PHE* 2.9 23.5 + - + +
334C HIS* 1.3 93.1 - - + +
336C PRO* 1.3 69.6 - - + +
338C LEU* 3.0 11.4 + - - +
339C SER* 2.9 24.6 + - - +
343C ALA* 5.5 0.3 - - - +
345C ALA* 4.1 28.0 - - + +
347C ILE* 4.1 20.0 - - + -
352C VAL* 4.1 18.6 - - + -
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Residues in contact with PRO 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C PHE 3.2 10.5 - - - +
333C MET* 2.9 22.9 - - - +
335C VAL* 1.3 86.7 - - + +
337C GLU* 1.3 61.4 + - - +
339C SER* 3.0 20.1 + - - +
340C ARG* 3.2 16.5 + - - +
347C ILE* 5.1 6.1 - - + -
111D LEU* 5.1 0.7 - - - +
112D PRO 4.8 4.5 - - - +
113D GLY* 3.7 8.9 - - - +
114D GLY* 3.7 28.5 - - - +
119D ALA* 5.9 3.6 - - + -
120D ARG 5.7 6.7 - - - +
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C MET* 3.7 13.9 - - + +
334C HIS* 3.1 9.5 + - - +
336C PRO* 1.3 75.3 - - - +
338C LEU* 1.3 63.8 + - - +
340C ARG* 3.0 27.3 + - - +
341C MET* 3.6 3.6 + - - +
365C VAL* 3.3 21.8 - - + +
366C MET* 2.9 49.0 + - - +
376C LEU* 3.7 20.4 - - + -
84D TYR* 5.2 1.4 + - - -
113D GLY* 3.7 7.0 - - - -
114D GLY* 3.2 23.9 + - - -
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C ALA 5.1 0.2 - - - +
311C THR* 4.8 0.7 - - + -
312C LEU* 4.2 27.4 - - + +
315C LEU* 3.6 23.3 - - + -
334C HIS* 2.9 34.1 + - + +
335C VAL* 3.6 6.7 - - - +
337C GLU* 1.3 75.3 - - - +
339C SER* 1.3 57.2 + - - +
341C MET* 2.9 26.6 + - - +
343C ALA* 3.2 29.8 + - + +
360C LEU* 4.9 2.9 - - + +
375C SER* 4.7 7.9 - - - +
376C LEU* 4.0 16.4 - - + -
379C ALA* 3.7 30.3 - - + -
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Residues in contact with SER 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C VAL* 2.9 20.4 + - - +
336C PRO* 3.0 16.5 + - - +
338C LEU* 1.3 78.3 - - - +
340C ARG* 1.3 58.8 + - - +
342C GLY* 3.1 11.8 + - - -
343C ALA* 3.6 21.4 + - - +
345C ALA* 4.8 10.0 + - - +
111D LEU* 4.1 14.4 - - - +
138D LEU* 3.4 15.2 - - - +
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Residues in contact with ARG 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C PRO 3.2 14.3 + - - +
337C GLU* 3.0 23.0 + - - +
339C SER* 1.3 76.2 - - - +
341C MET* 1.3 59.5 + - - +
342C GLY 3.3 1.0 + - - -
361C SER* 4.5 1.0 - - - +
363C ALA* 3.7 15.8 - - + +
364C GLN* 2.3 53.1 + - - +
365C VAL* 4.5 3.8 - - + -
84D TYR* 3.5 22.7 - - - +
110D SER* 3.2 22.4 + - - -
111D LEU* 3.1 33.9 + - + +
112D PRO 5.0 0.2 - - - +
113D GLY* 4.5 11.2 - - - +
138D LEU* 4.3 6.2 - - - +
140D GLU 4.1 3.6 + - - -
141D GLY* 3.2 39.6 + - - -
142D TYR* 5.2 2.2 - - - -
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Residues in contact with MET 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C GLU 4.1 6.5 - - - +
338C LEU* 2.9 19.8 + - - +
340C ARG* 1.3 79.5 - - - +
342C GLY* 1.3 56.1 + - - +
343C ALA 3.5 1.8 - - - -
360C LEU* 3.5 15.9 - - + +
361C SER* 2.7 46.3 + - - +
363C ALA* 4.2 6.7 - - + +
365C VAL* 4.1 24.2 - - + -
376C LEU* 4.9 2.2 - - - +
379C ALA* 3.6 33.9 - - + -
380C GLY* 3.9 1.3 - - - +
383C ALA* 3.5 31.0 - - + -
387C THR* 3.6 23.3 - - - +
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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