Contacts of the helix formed by residues 333 - 341 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F THR* 3.5 45.8 - - + +
117F ILE* 5.6 2.9 - - + -
330F ASN 4.6 4.9 + - - +
331F ARG 3.9 1.0 - - - -
332F PHE* 1.3 76.8 - - - +
334F HIS* 1.3 57.1 + - - +
336F PRO* 3.0 21.4 - - + +
337F GLU* 3.7 15.4 - - + +
368F THR* 4.0 35.7 - - + +
369F ASP* 6.3 1.6 - - + -
114G GLY* 4.3 8.1 - - - -
115G QPA 3.7 38.8 - - - +
116G THR* 4.1 11.0 - - + -
118G GLY 6.4 0.9 - - - -
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Residues in contact with HIS 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F GLN* 2.9 30.5 + - - -
308F ALA* 3.4 32.1 - - + +
311F THR* 3.6 14.1 + - + -
331F ARG* 3.2 22.7 + - - +
332F PHE* 3.9 7.9 - + - -
333F MET* 1.3 72.2 + - - +
335F VAL* 1.3 77.0 + - + +
337F GLU* 3.2 10.4 + - - +
338F LEU* 2.9 37.7 + - + +
372F ALA* 4.1 16.3 - - + +
373F SER* 5.8 2.0 - - - +
375F SER* 4.0 15.0 - - - +
376F LEU* 4.6 9.9 - - + -
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Residues in contact with VAL 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F THR* 4.3 7.9 - - + -
315F LEU* 5.6 2.4 - - + +
332F PHE* 3.0 17.1 + - + +
334F HIS* 1.3 92.7 - - + +
336F PRO* 1.3 71.0 - - + +
338F LEU* 3.1 10.0 + - - +
339F SER* 2.9 23.9 + - - +
343F ALA* 5.5 0.3 - - - +
345F ALA* 4.1 28.7 - - + +
347F ILE* 4.0 24.7 - - + -
352F VAL* 4.0 19.1 - - + -
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Residues in contact with PRO 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F PHE 3.2 10.1 - - - +
333F MET* 3.0 24.0 - - - +
335F VAL* 1.3 86.9 - - + +
337F GLU* 1.3 60.7 + - - +
339F SER* 3.0 19.8 + - - +
340F ARG* 3.2 15.7 + - - +
347F ILE* 5.1 6.3 - - + -
91G ARG* 5.9 0.7 - - - +
112G PRO 4.5 4.6 - - - +
113G GLY* 3.7 10.7 - - - +
114G GLY* 3.6 26.5 - - - +
115G QPA 5.4 0.2 - - - +
118G GLY 5.9 0.7 - - - +
119G ALA* 5.4 4.0 - - - -
120G ARG 5.3 12.3 - - - +
121G PRO 6.3 0.2 - - - -
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F MET* 3.7 14.4 - - + +
334F HIS* 3.2 9.9 + - - +
336F PRO* 1.3 77.1 - - - +
338F LEU* 1.3 62.5 + - - +
340F ARG* 3.0 28.6 + - - +
341F MET* 3.6 3.5 + - - +
365F VAL* 3.4 22.2 - - + +
366F MET* 2.9 48.5 + - - +
376F LEU* 3.6 19.7 - - + -
84G TYR* 5.2 1.0 + - - -
113G GLY* 3.5 6.0 - - - -
114G GLY* 2.8 27.8 + - - +
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Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F THR* 4.8 0.4 - - + -
312F LEU* 4.3 26.7 - - + +
315F LEU* 3.6 24.2 - - + -
334F HIS* 2.9 32.8 + - + +
335F VAL* 3.7 6.3 - - - +
337F GLU* 1.3 74.8 - - - +
339F SER* 1.3 57.7 + - - +
341F MET* 2.9 27.1 + - - +
343F ALA* 3.2 29.8 + - + +
360F LEU* 4.9 3.0 - - + +
375F SER* 4.5 8.1 - - - +
376F LEU* 4.0 16.4 - - + -
379F ALA* 3.7 30.5 - - + -
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Residues in contact with SER 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F VAL* 2.9 21.3 + - - +
336F PRO* 3.0 15.8 + - - +
338F LEU* 1.3 73.5 - - - +
340F ARG* 1.3 58.6 - - - +
341F MET 3.0 5.4 - - - -
342F GLY* 3.2 11.1 + - - -
343F ALA* 3.7 21.3 + - - +
345F ALA* 4.8 9.7 + - - +
111G LEU* 3.6 15.6 - - - +
138G LEU* 3.4 13.3 - - - +
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Residues in contact with ARG 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F PRO 3.2 14.1 + - - +
337F GLU* 3.0 18.5 + - - +
339F SER* 1.3 75.9 - - - +
341F MET* 1.3 59.3 + - - +
342F GLY 3.4 1.2 + - - -
361F SER* 4.5 1.2 - - - +
363F ALA* 3.7 9.7 - - + +
364F GLN* 2.3 49.4 + - - +
365F VAL* 4.5 3.8 - - + -
84G TYR* 3.4 20.8 - - - +
110G SER* 2.7 27.3 + - - -
111G LEU* 2.7 37.0 + - + +
112G PRO 4.5 0.4 - - - +
113G GLY* 4.1 15.9 - - - +
138G LEU* 4.1 5.7 - - - +
140G GLU 4.6 2.6 + - - -
141G GLY* 3.2 44.6 + - - -
142G TYR* 5.4 1.6 - - - -
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Residues in contact with MET 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F GLU 4.0 6.1 - - - +
338F LEU* 2.9 19.2 + - - +
340F ARG* 1.3 79.5 - - - +
342F GLY* 1.3 57.8 + - - +
343F ALA 3.6 1.8 - - - -
360F LEU* 3.5 15.6 - - + +
361F SER* 2.7 45.7 + - - +
363F ALA* 4.1 7.2 - - + +
365F VAL* 4.0 25.4 - - + -
376F LEU* 4.9 2.0 - - - +
379F ALA* 3.6 34.5 - - + -
380F GLY 3.9 1.1 - - - +
383F ALA* 3.6 23.1 - - + -
387F THR* 3.5 29.6 - - + +
138G LEU* 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