Contacts of the helix formed by residues 365 - 379 (chain P) in PDB entry 3H1I
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 ILE 365 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361P THR* 2.7 36.5 + - + +
363P LEU 3.5 0.4 - - - -
364P LEU* 1.3 83.3 - - + +
366P LEU* 1.3 82.0 + - + +
368P PRO* 2.9 12.9 - - - +
369P THR* 2.9 27.9 + - + +
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Residues in contact with LEU 366 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325P LEU* 3.3 37.2 - - + -
328P LEU* 5.7 2.5 - - + -
361P THR* 2.9 28.0 + - + +
362P ILE* 3.8 15.9 - - + +
365P ILE* 1.3 86.0 - - + +
367P PHE* 1.3 57.5 + - - +
369P THR* 2.8 5.8 + - - -
370P ILE* 2.6 37.8 + - + +
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Residues in contact with PHE 367 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P LEU* 4.3 14.1 - - + -
305P ILE* 5.6 2.5 - - + -
308P LEU 4.9 8.2 - - - +
310P LYS 5.7 0.7 + - - -
316P MET* 3.5 33.4 - - + -
319P ARG* 5.6 1.6 + - - -
322P SER* 3.9 10.0 + - - -
325P LEU* 3.8 30.5 - - + -
326P PHE* 3.7 21.8 - + + -
329P LEU* 4.3 10.5 - - + -
362P ILE* 2.9 29.5 + - + +
363P LEU* 4.0 30.3 - - + +
366P LEU* 1.3 72.4 - - - +
368P PRO* 1.3 66.8 - - + +
370P ILE* 4.5 1.0 - - + +
371P GLY* 3.2 18.9 + - - -
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Residues in contact with PRO 368 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308P LEU* 4.4 23.1 - - + +
310P LYS* 3.6 31.2 - - + +
363P LEU 3.8 9.9 - - - +
364P LEU 3.5 16.2 - - - +
365P ILE* 2.9 32.1 - - - +
367P PHE* 1.3 90.7 - - + +
369P THR* 1.3 56.8 + - - +
372P THR* 3.1 30.3 + - - -
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Residues in contact with THR 369 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365P ILE* 2.9 26.6 + - + +
366P LEU* 2.8 6.0 + - - -
368P PRO* 1.3 75.6 - - - +
370P ILE* 1.3 67.4 + - + +
371P GLY 2.8 5.6 + - - -
372P THR* 2.9 16.2 + - - -
373P LEU* 3.0 18.1 + - + +
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Residues in contact with ILE 370 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321P LEU* 3.4 43.7 - - + +
322P SER* 3.9 15.0 - - - +
325P LEU* 3.7 22.0 - - + -
366P LEU* 2.6 24.5 + - + +
367P PHE* 4.5 2.2 - - + +
369P THR* 1.3 75.1 - - + +
371P GLY* 1.3 54.3 + - - +
373P LEU* 3.8 16.2 - - + +
374P GLU* 3.0 27.7 + - - +
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Residues in contact with GLY 371 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310P LYS* 4.6 4.3 - - - -
311P SER* 4.5 7.1 - - - -
319P ARG* 4.7 7.0 - - - -
322P SER* 4.7 2.7 + - - -
367P PHE 3.2 18.5 + - - -
368P PRO 3.8 1.6 - - - -
369P THR 2.8 3.0 - - - -
370P ILE* 1.3 75.8 - - - +
372P THR* 1.3 65.9 + - - +
374P GLU* 3.0 30.6 - - - +
375P ASN* 3.2 12.6 + - - +
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Residues in contact with THR 372 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310P LYS* 4.0 17.2 - - - +
368P PRO 3.1 13.7 + - - -
369P THR* 2.9 9.8 + - - -
371P GLY* 1.3 72.4 - - - +
373P LEU* 1.3 67.8 + - - +
375P ASN* 2.9 28.4 + - - +
376P LYS* 3.5 29.8 + - + +
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Residues in contact with LEU 373 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321P LEU* 4.9 8.7 - - + -
369P THR* 3.0 18.1 + - + +
370P ILE* 3.8 22.4 - - + +
372P THR* 1.3 80.7 - - - +
374P GLU* 1.3 62.9 + - - +
376P LYS* 3.2 25.4 + - + +
377P MET* 3.2 27.7 + - + +
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Residues in contact with GLU 374 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311P SER* 4.3 0.8 + - - +
319P ARG* 2.8 43.5 - - + +
321P LEU* 3.3 12.5 - - + +
322P SER* 2.8 37.6 + - - -
370P ILE 3.0 19.6 + - - +
371P GLY* 3.0 17.6 - - - +
372P THR 2.9 1.2 + - - -
373P LEU* 1.3 76.5 - - - +
375P ASN* 1.3 61.3 + - - +
377P MET* 3.3 11.7 + - - +
378P LEU* 3.3 24.7 + - + +
20S TYR* 3.1 26.2 + - + +
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Residues in contact with ASN 375 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310P LYS 3.4 20.8 + - - -
311P SER* 3.4 9.5 + - - -
312P LYS* 2.9 46.5 + - + +
313P GLN* 5.5 1.2 - - - +
371P GLY 3.2 16.1 + - - +
372P THR* 2.9 18.6 + - - +
374P GLU* 1.3 69.1 - - - +
376P LYS* 1.3 57.6 + - + +
377P MET 3.1 1.6 - - - -
378P LEU* 3.1 11.5 + - - +
379P ASN 2.7 27.4 + - - -
380P TYR* 2.7 23.0 + - + +
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Residues in contact with LYS 376 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372P THR* 4.1 29.1 - - + +
373P LEU* 3.2 17.3 + - + +
375P ASN* 1.3 78.3 - - + +
377P MET* 1.3 61.8 + - + +
379P ASN* 3.2 12.7 + - - +
380P TYR 4.2 13.7 + - - +
17S ARG* 3.5 20.4 + - - +
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Residues in contact with MET 377 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321P LEU* 4.4 15.5 - - + -
373P LEU* 3.2 29.9 + - + +
374P GLU 3.5 8.7 - - - +
375P ASN 3.1 0.6 - - - -
376P LYS* 1.3 79.7 - - + +
378P LEU* 1.3 61.8 + - - +
379P ASN 3.1 0.2 - - - -
16S ILE* 3.8 25.4 - - + -
17S ARG* 3.4 33.4 - - - +
19S TRP* 4.0 17.5 - - + -
20S TYR* 3.2 50.5 - - + +
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Residues in contact with LEU 378 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313P GLN* 3.6 38.1 - - + +
318P PHE 5.4 0.2 - - - +
374P GLU* 3.3 8.7 + - + +
375P ASN* 3.1 13.3 + - - +
377P MET* 1.3 77.9 - - - +
379P ASN* 1.3 68.7 + - - +
380P TYR* 4.4 19.7 - - + -
17S ARG* 5.4 0.7 - - - -
20S TYR* 3.6 34.5 - - + +
21S TYR* 4.9 11.2 - - + -
26S PHE* 4.1 24.7 - - + -
33S ARG* 3.2 28.2 + - + -
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Residues in contact with ASN 379 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375P ASN 2.7 6.5 + - - -
376P LYS* 3.2 9.6 + - - +
377P MET 3.1 3.0 - - - -
378P LEU* 1.3 83.9 - - - +
380P TYR* 1.3 61.8 + - - +
17S ARG* 3.4 35.0 + - - +
33S ARG* 3.7 16.3 + - - +
91S GLU* 4.0 14.8 + - - +
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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