Contacts of the helix formed by residues 348 - 366 (chain A) in PDB entry 4L7F
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 THR 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.8 3.1 - - - +
347A HIS* 1.3 75.7 - - - +
349A ILE* 1.3 59.1 + - - +
350A GLU* 3.4 9.3 + - - +
351A GLU* 2.9 40.3 + - + +
352A TRP* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.1 35.6 - - + +
62A GLN* 3.7 19.3 - - - +
63A ASN* 4.3 11.2 - - + -
64A GLN* 3.8 16.9 - - + +
348A THR* 1.3 72.3 - - - +
350A GLU* 1.3 58.4 + - - +
352A TRP* 3.4 6.8 + - - +
353A LYS* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.9 11.4 - - - +
348A THR* 3.2 8.3 + - - +
349A ILE* 1.3 80.2 - - - +
351A GLU* 1.3 61.1 + - + +
353A LYS* 3.4 27.2 + - - +
354A GLU* 3.1 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU 4.4 1.6 - - - +
347A HIS* 3.3 24.9 + - + +
348A THR* 2.9 50.0 + - - +
350A GLU* 1.3 74.8 - - + +
352A TRP* 1.3 58.9 + - - +
354A GLU* 3.3 17.9 + - - +
355A LEU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.7 1.6 - - + -
64A GLN* 3.0 32.1 + - - +
67A ALA* 3.5 33.5 - - + +
68A LYS* 3.8 41.1 - - + -
71A TYR* 3.8 41.7 - + + -
345A ARG 4.5 5.6 - - - -
346A GLU* 5.6 0.2 - - - -
347A HIS* 3.4 35.2 + + + +
348A THR 2.9 22.3 + - - -
349A ILE* 3.6 9.2 - - - +
351A GLU* 1.3 72.5 - - - +
353A LYS* 1.3 61.4 + - - +
355A LEU* 3.2 19.5 + - + +
356A ILE* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.7 45.0 - - + +
98A LEU* 3.1 32.9 + - + +
99A GLU* 3.7 15.2 + - - +
101A PHE* 3.7 26.9 + - + -
102A GLN* 5.8 0.4 - - - +
349A ILE* 2.9 17.5 + - + +
350A GLU* 3.4 31.0 + - - +
352A TRP* 1.3 77.9 - - - +
354A GLU* 1.3 56.4 + - - +
356A ILE* 4.0 1.1 - - - +
357A TYR* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.4 33.0 - - + +
350A GLU* 3.1 37.8 + - - +
351A GLU* 3.6 17.0 - - - +
352A TRP 3.3 0.2 - - - -
353A LYS* 1.3 72.4 - - - +
355A LEU* 1.3 61.6 + - + +
357A TYR* 3.8 2.0 - - - +
358A LYS* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.5 39.6 - - + +
347A HIS* 3.7 33.2 - - + +
351A GLU* 3.0 18.1 + - + +
352A TRP* 3.2 33.0 + - + +
354A GLU* 1.3 78.7 - - - +
356A ILE* 1.3 57.5 + - - +
358A LYS* 3.6 11.1 + - + +
359A GLU* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 4.3 16.4 - - + -
61A PHE* 4.5 4.5 - - + +
67A ALA* 3.8 35.2 - - + +
70A ALA* 4.2 10.5 - - + -
71A TYR* 4.1 22.9 - - + +
74A LEU* 4.0 13.7 - - + -
101A PHE* 3.8 21.3 - - + -
104A VAL* 4.0 14.6 - - + -
352A TRP* 2.9 22.5 + - + +
353A LYS 4.0 2.9 - - - +
355A LEU* 1.3 75.0 - - + +
357A TYR* 1.3 67.0 + - - +
359A GLU* 3.1 7.9 + - - +
360A VAL* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 4.5 13.5 - - + -
95A GLN 4.8 1.6 + - - -
96A LYS 4.0 5.0 + - - -
97A SER* 3.5 31.5 + - - -
98A LEU* 3.6 35.0 - - + -
101A PHE* 3.7 37.2 - + + -
353A LYS 3.0 18.8 + - - +
354A GLU 3.8 2.7 - - - +
356A ILE* 1.3 77.5 - - - +
358A LYS* 1.3 58.6 + - - +
360A VAL* 3.2 5.1 + - + +
361A MET* 2.9 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLN* 6.0 1.8 - - - +
354A GLU 2.9 18.5 + - - +
355A LEU* 3.7 11.7 - - + +
356A ILE 3.3 0.2 - - - -
357A TYR* 1.3 78.8 - - - +
359A GLU* 1.3 57.2 + - - +
361A MET* 3.3 5.3 + - - +
362A ASP* 2.8 68.1 + - - +
365A LYS* 6.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 4.4 4.7 + - + -
74A LEU* 3.8 30.4 - - + +
75A VAL* 3.9 21.8 - - + +
78A LYS* 3.4 31.4 + - - -
91A VAL* 5.0 1.8 - - - +
341A GLN* 2.8 32.3 + - - +
355A LEU 3.1 14.7 + - - +
356A ILE* 3.1 11.4 + - - +
358A LYS* 1.3 75.4 - - - +
360A VAL* 1.3 64.8 + - - +
362A ASP* 3.4 12.9 + - - +
363A TRP* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.5 7.9 - - + -
91A VAL* 4.5 11.9 - - + +
92A PHE* 3.9 12.8 - - - +
93A THR* 3.8 39.7 - - + +
101A PHE* 4.4 4.0 - - + -
104A VAL* 3.9 35.2 - - + -
356A ILE 3.0 19.0 + - - +
357A TYR* 3.6 8.5 - - + +
359A GLU* 1.3 76.1 - - - +
361A MET* 1.3 67.4 + - - +
363A TRP* 3.2 19.9 + - - +
364A ARG* 3.8 6.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 4.7 13.9 - - - -
95A GLN 5.8 0.7 - - - +
357A TYR* 2.9 55.7 + - + +
358A LYS* 4.0 4.9 - - + +
360A VAL* 1.3 80.8 - - - +
362A ASP* 1.3 62.4 + - - +
364A ARG* 3.1 30.8 + - + +
365A LYS* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 4.2 17.1 + - - +
341A GLN* 5.6 0.7 + - - -
358A LYS* 2.8 58.3 + - - +
359A GLU* 3.6 16.5 - - - +
360A VAL 3.3 0.2 - - - -
361A MET* 1.3 73.4 - - - +
363A TRP* 1.3 62.7 + - - +
365A LYS* 3.7 23.0 + - - +
366A GLY* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.8 33.8 - - + +
88A LEU* 3.8 37.2 - - + -
89A LEU 3.5 20.4 - - - -
90A ASN* 3.1 21.5 + - - -
91A VAL* 3.4 42.4 - - + +
359A GLU 3.4 5.5 + - - +
360A VAL 3.2 13.5 + - - +
361A MET 3.1 0.4 - - - -
362A ASP* 1.3 78.6 - - - +
364A ARG* 1.3 71.0 + - - +
366A GLY* 3.3 10.4 + - - -
367A ILE* 3.4 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 4.7 16.2 + - - -
90A ASN* 4.9 4.2 + - - -
91A VAL 5.1 4.9 - - - -
92A PHE* 5.8 4.9 - - - +
360A VAL* 3.8 6.7 + - + +
361A MET* 3.1 33.7 + - + +
363A TRP* 1.3 86.0 - - - +
365A LYS* 1.3 65.7 + - + +
367A ILE* 2.9 53.2 + - - +
368A ILE* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 6.1 3.0 - - - +
361A MET* 3.0 20.2 + - - +
362A ASP* 3.3 28.3 + - - +
364A ARG* 1.3 77.1 - - + +
366A GLY* 1.3 59.4 + - - +
367A ILE 3.5 0.9 + - - -
368A ILE* 4.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASP 3.0 13.8 + - - -
363A TRP 3.3 4.0 + - - -
364A ARG 3.1 0.6 - - - -
365A LYS* 1.3 75.8 - - - +
367A ILE* 1.3 63.6 + - - +
368A ILE 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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