Contacts of the helix formed by residues 310 - 328 (chain A) in PDB entry 3W5D
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 GLY 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A PRO 3.2 1.0 - - - -
309A GLU* 1.3 78.7 - - - +
311A LEU* 1.3 64.0 + - - +
312A PRO* 3.4 1.6 - - - -
313A ALA* 3.2 11.1 + - - +
314A VAL* 3.1 29.5 + - - +
764A LEU* 4.6 2.2 - - - +
796A ASN 3.3 24.0 + - - -
797A LEU* 3.7 12.7 - - - +
801A GLY* 6.1 0.4 - - - -
1002A PTY 6.1 0.9 - - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 5.1 13.0 - - + -
256A PHE* 5.9 2.0 - - + -
308A PRO* 2.9 40.9 + - + +
310A GLY* 1.3 76.5 - - - +
312A PRO* 1.4 61.1 - - + +
314A VAL* 3.1 2.1 + - + +
315A ILE* 3.0 52.1 + - + +
760A PHE* 4.3 7.9 - - + -
761A ILE* 4.1 34.3 - - + +
764A LEU* 3.8 23.8 - - + +
765A ILE* 4.9 7.6 - - + -
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Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 5.7 4.3 - - - +
308A PRO 3.7 4.0 - - - +
309A GLU 3.6 16.4 - - - +
311A LEU* 1.4 95.9 - - + +
313A ALA* 1.3 60.2 + - - +
315A ILE* 3.8 8.5 - - + +
316A THR* 2.9 30.0 + - - -
1002A PTY 3.7 49.1 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLY* 3.2 12.7 + - - +
312A PRO* 1.3 77.0 - - - +
314A VAL* 1.3 58.9 + - + +
316A THR* 3.7 2.1 - - - -
317A THR* 2.6 38.5 + - - +
1002A PTY 3.4 44.9 - - + +
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Residues in contact with VAL 314 (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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310A GLY 3.1 16.8 + - - +
311A LEU* 3.1 8.8 + - - +
313A ALA* 1.3 73.8 - - + +
315A ILE* 1.3 66.9 + - - +
317A THR* 3.2 4.9 + - - -
318A CYS* 2.9 22.7 + - + +
760A PHE* 3.8 18.4 - - + -
764A LEU* 4.3 4.9 - - + -
801A GLY* 3.8 31.6 - - - +
804A ALA* 3.7 27.1 - - + +
805A THR* 3.7 23.4 + - - +
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Residues in contact with ILE 315 (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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249A LEU* 4.6 11.7 - - + -
253A LEU* 3.9 28.9 - - + -
311A LEU* 3.0 41.7 + - + +
312A PRO* 3.8 8.1 - - + +
314A VAL* 1.3 74.7 - - - +
316A THR* 1.3 60.7 + - - +
318A CYS* 3.0 4.0 + - - +
319A LEU* 2.8 49.7 + - + +
757A MET* 4.5 9.2 - - - -
760A PHE* 3.9 18.2 - - + -
761A ILE* 4.8 5.2 - - + -
1002A PTY 5.8 7.6 - - - +
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN* 6.2 0.4 - - - +
312A PRO 2.9 13.2 + - - -
313A ALA* 3.7 4.0 - - - -
315A ILE* 1.3 79.9 - - - +
317A THR* 1.3 60.6 + - - +
319A LEU* 3.3 5.8 + - - +
320A ALA* 2.8 33.0 + - + +
336A LEU* 4.4 18.1 - - + +
1002A PTY 2.9 48.2 + - - +
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA* 2.6 25.0 + - - +
314A VAL* 3.5 7.4 - - - -
316A THR* 1.3 77.7 - - - +
318A CYS* 1.3 59.5 + - - +
320A ALA* 3.6 5.4 + - - +
321A LEU* 2.9 44.1 + - + +
805A THR* 3.9 25.5 + - + +
1002A PTY 5.4 2.1 + - - -
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Residues in contact with CYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 2.9 12.5 + - + +
315A ILE 3.0 8.5 + - - +
317A THR* 1.3 75.9 - - - +
319A LEU* 1.3 61.5 + - + +
321A LEU* 3.0 10.2 + - - +
322A GLY* 2.8 27.7 + - - -
325A ARG* 5.2 2.9 + - - -
753A ILE* 4.1 24.2 - - - +
756A ASN* 5.7 0.4 - - - -
757A MET* 4.4 4.0 - - - -
760A PHE* 3.8 30.5 - - + -
805A THR* 5.5 5.4 - - + +
808A GLY* 4.4 19.7 - - - -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 6.0 2.0 - - + -
315A ILE* 2.8 34.9 + - + +
316A THR* 3.7 5.2 - - - +
318A CYS* 1.3 77.1 - - - +
320A ALA* 1.3 62.4 + - - +
322A GLY* 3.4 1.5 + - - +
323A THR* 2.9 28.1 + - - -
336A LEU* 3.4 49.6 - - + +
337A PRO* 4.4 5.4 - - + -
339A VAL* 4.5 13.1 - - + +
340A GLU* 5.7 2.0 - - + +
753A ILE* 4.1 16.8 - - + -
757A MET* 3.6 32.1 - - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 2.8 25.8 + - + +
317A THR* 3.9 6.7 - - - +
319A LEU* 1.3 72.5 - - - +
321A LEU* 1.3 66.1 + - + +
323A THR* 3.4 4.8 - - - +
324A ARG* 3.1 26.4 + - - +
336A LEU* 4.0 17.4 - - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 2.9 37.8 + - + +
318A CYS* 3.0 8.3 + - - +
320A ALA* 1.3 77.0 - - + +
322A GLY* 1.3 64.7 + - - +
324A ARG* 3.2 26.4 + - + +
325A ARG* 3.1 31.3 + - - +
805A THR* 4.7 7.0 - - + -
809A PHE* 3.5 33.4 - - + -
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A CYS 2.8 13.8 + - - -
319A LEU 3.8 2.0 - - - -
321A LEU* 1.3 76.5 - - - +
323A THR* 1.3 50.0 + - - +
325A ARG* 2.9 22.8 + - - +
326A MET* 2.7 43.1 + - - +
339A VAL* 5.8 0.2 - - - -
753A ILE* 3.8 22.0 - - - -
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Residues in contact with THR 323 (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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319A LEU 2.9 20.0 + - - -
320A ALA* 3.4 6.7 - - - +
322A GLY* 1.3 71.5 - - - +
324A ARG* 1.3 68.1 + - + +
326A MET* 3.2 14.0 + - - +
327A ALA* 3.0 24.1 + - + +
331A ALA 4.6 1.2 - - - +
333A VAL* 4.3 26.0 + - + +
336A LEU* 3.4 21.1 - - + +
339A VAL* 3.9 14.1 - - - +
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Residues in contact with ARG 324 (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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320A ALA* 3.1 17.5 + - - +
321A LEU* 3.2 25.2 + - - +
323A THR* 1.3 77.3 - - + +
325A ARG* 1.3 60.9 + - - +
327A ALA* 3.5 7.8 + - - +
328A LYS* 3.3 24.9 + - - +
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Residues in contact with ARG 325 (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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318A CYS* 5.2 3.0 + - - -
321A LEU* 3.1 13.9 + - - +
322A GLY* 2.9 29.0 + - - +
324A ARG* 1.3 77.5 - - - +
326A MET* 1.3 59.7 + - - +
328A LYS* 3.4 20.8 - - + +
329A LYS* 3.6 23.0 + - - +
749A GLU* 2.8 37.8 + - - +
752A ALA* 5.8 1.2 - - - +
753A ILE* 3.8 22.8 - - - +
808A GLY 4.6 9.7 + - - -
809A PHE* 4.2 27.6 - - - +
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Residues in contact with MET 326 (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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322A GLY 2.7 17.3 + - - +
323A THR* 3.7 17.9 - - - +
325A ARG* 1.3 70.2 - - - +
327A ALA* 1.3 61.6 + - - +
328A LYS 3.2 0.4 - - - -
329A LYS* 3.0 19.7 + - - +
330A ASN 3.3 0.2 + - - -
331A ALA* 2.9 37.4 + - + +
333A VAL* 3.2 31.4 - - + -
339A VAL* 3.5 36.8 - - + -
342A LEU* 4.6 2.7 - - + -
746A ALA* 4.3 17.0 - - - +
749A GLU* 3.4 36.3 - - + -
753A ILE* 4.8 0.2 - - - -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A THR* 3.0 17.1 + - + +
324A ARG* 3.7 9.6 - - - +
326A MET* 1.3 73.1 - - - +
328A LYS* 1.3 65.4 - - - +
329A LYS 3.0 0.4 - - - -
330A ASN* 3.0 18.5 + - - +
331A ALA 3.2 13.6 + - - +
332A ILE* 4.8 14.9 - - + +
333A VAL 6.0 0.2 - - - +
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Residues in contact with LYS 328 (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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324A ARG 3.3 13.5 + - - +
325A ARG* 3.4 13.9 - - + +
326A MET 3.2 0.6 - - - -
327A ALA* 1.3 80.7 - - - +
329A LYS* 1.3 60.7 + - + +
330A ASN* 3.3 5.7 + - - -
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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
------------------------------------------------------------
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