Contacts of the helix formed by residues 1003 - 1020 (chain B) in PDB entry 4E70
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 ALA1003 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 4.6 7.4 - - - +
192A SER* 3.5 34.8 - - - +
1001B MET 3.9 0.6 + - - -
1002B ASP* 1.3 74.6 - - - +
1004B ALA* 1.3 63.8 + - - +
1006B ALA* 3.2 7.5 + - - +
1007B VAL* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1004 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ASP* 3.2 15.4 - - - +
1003B ALA* 1.3 78.1 - - - +
1005B THR* 1.3 62.7 + - - +
1007B VAL* 3.5 5.8 + - - +
1008B GLU* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.5 12.8 - - - +
1001B MET* 3.7 21.5 - - + -
1002B ASP* 2.6 28.2 + - - -
1004B ALA* 1.3 73.6 - - - +
1006B ALA* 1.3 66.2 + - - +
1008B GLU* 3.3 10.6 + - + +
1009B LEU* 3.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.0 16.2 - - + +
188A ARG* 3.6 31.9 - - + -
189A ALA* 4.4 3.6 - - - +
1001B MET* 3.6 19.9 - - + -
1002B ASP 3.1 13.3 + - - +
1003B ALA* 3.2 9.2 + - - +
1005B THR* 1.3 76.3 - - - +
1007B VAL* 1.3 57.2 + - - +
1009B LEU* 3.4 2.4 + - - +
1010B LEU* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1007 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 3.6 27.6 - - + +
192A SER* 5.4 1.3 - - - +
193A LYS* 4.0 31.0 - - + +
357A VAL 4.4 6.1 - - - +
1003B ALA* 2.9 24.6 + - + +
1004B ALA* 3.8 5.4 - - - +
1006B ALA* 1.3 73.2 - - - +
1008B GLU* 1.3 66.1 + - - +
1010B LEU* 3.2 8.0 + - + +
1011B ASP* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1008 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 5.5 0.5 - - - +
105A ARG* 2.9 36.2 + - - +
1004B ALA 3.1 17.4 + - - +
1005B THR* 3.6 9.3 - - - +
1007B VAL* 1.3 77.1 - - - +
1009B LEU* 1.3 57.9 + - - +
1011B ASP* 3.3 7.8 + - - +
1012B ALA* 3.0 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1009 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 5.2 0.4 - - - +
105A ARG* 3.6 50.9 - - + +
106A LEU* 4.1 20.3 - - + +
113A TYR* 3.7 18.2 - - + +
185A LEU* 3.9 15.9 - - + +
1001B MET* 3.7 32.3 - - + -
1005B THR* 3.0 24.8 + - + +
1006B ALA 3.8 3.1 - - - +
1008B GLU* 1.3 72.8 - - + +
1010B LEU* 1.3 66.3 + - - +
1012B ALA* 3.0 15.7 + - + +
1013B GLN* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1010 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASP* 4.2 0.2 - - - +
185A LEU* 4.0 12.9 - - + +
186A PHE* 3.9 31.4 - - + +
189A ALA* 3.6 27.8 - - + -
357A VAL* 4.1 1.3 - - + +
358A GLY* 3.5 27.1 - - - +
359A GLY* 3.5 11.2 - - - +
361A ARG* 3.6 18.2 - - - +
1006B ALA 2.8 18.7 + - - +
1007B VAL* 3.4 5.6 - - - +
1009B LEU* 1.3 74.7 - - - +
1011B ASP* 1.3 61.1 + - - +
1013B GLN* 3.4 27.8 + - - +
1014B PRO* 3.3 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1011 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL 5.0 0.2 - - - +
358A GLY* 3.2 11.3 - - - -
359A GLY* 2.8 23.8 + - - -
1007B VAL* 2.9 32.4 + - - +
1008B GLU* 3.8 6.4 - - - +
1010B LEU* 1.3 76.0 - - - +
1012B ALA* 1.3 58.2 + - - +
1014B PRO* 3.4 14.9 - - - +
1015B GLN* 4.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1012 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.9 22.2 - - + +
105A ARG* 5.4 6.1 - - - +
106A LEU* 4.0 8.3 - - + -
1008B GLU* 3.0 14.1 + - + +
1009B LEU* 3.0 14.5 + - + +
1011B ASP* 1.3 79.1 - - - +
1013B GLN* 1.3 65.7 + - - +
1014B PRO 3.3 0.9 - - - -
1015B GLN* 3.1 33.3 + - - +
1016B VAL* 3.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1013 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.8 19.5 - - + +
113A TYR 4.3 8.8 - - - +
115A ALA* 5.2 8.1 - - + +
118A LEU* 6.1 0.3 - - - +
182A ASP* 2.9 41.5 + - - +
185A LEU* 3.8 19.4 - - + +
361A ARG* 4.1 0.2 - - - +
1009B LEU 3.1 19.6 + - - +
1010B LEU* 3.4 22.1 + - - +
1012B ALA* 1.3 76.3 - - - +
1014B PRO* 1.3 68.9 - - + +
1016B VAL* 2.8 17.0 + - - +
1017B TRP* 3.0 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1014 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 6.2 0.7 - - - -
318A THR* 3.6 10.0 + - + +
359A GLY* 3.9 14.1 - - - -
360A LEU* 3.7 41.3 - - + +
1010B LEU 3.3 12.8 - - - +
1011B ASP 3.4 15.9 - - - +
1012B ALA 3.4 0.2 - - - -
1013B GLN* 1.3 91.1 - - + +
1015B GLN* 1.3 55.1 + - - +
1017B TRP* 3.6 17.5 - - + +
1018B HIS* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1015 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 5.6 0.5 - - - +
103A LEU* 4.1 25.4 - - + +
1011B ASP 4.3 4.9 + - - +
1012B ALA* 3.1 29.9 + - - +
1014B PRO* 1.3 77.7 - - + +
1016B VAL* 1.3 62.0 + - - +
1018B HIS* 3.4 7.5 + - - +
1019B HIS* 3.2 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1016 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.0 8.1 - - + -
79A TYR* 3.5 31.0 - - + +
103A LEU* 4.0 16.2 - - + -
106A LEU* 3.8 31.4 - - + -
107A LEU* 4.8 6.1 - - + -
115A ALA* 4.4 16.4 - - + -
119A THR* 4.6 1.8 - - - +
1012B ALA 4.1 0.4 - - - +
1013B GLN* 2.8 9.2 + - - +
1015B GLN* 1.3 75.0 - - - +
1017B TRP* 1.3 67.2 + - + +
1019B HIS* 3.1 3.8 + - - +
1020B PHE* 2.9 39.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1017 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 5.6 4.1 - - + +
118A LEU* 3.8 16.3 - - + +
182A ASP* 3.7 18.4 - - + -
268A TRP* 3.8 21.3 - + - -
303A HIS* 4.9 0.7 - + - -
318A THR* 4.3 5.6 - - + -
322A LEU* 4.0 25.6 - - + -
359A GLY* 3.9 15.0 - - - -
360A LEU* 4.0 13.9 - - + -
361A ARG* 3.6 21.8 - - - -
403A N7I 5.3 3.1 - + - -
1013B GLN* 3.0 34.2 + - + +
1014B PRO* 3.6 24.5 - - + +
1016B VAL* 1.3 75.9 - - + +
1018B HIS* 1.3 58.7 + - - +
1020B PHE* 3.4 32.5 - + + -
1021B LEU* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1018 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 5.5 1.2 + - - -
314A ASN* 4.5 5.2 + - - -
317A GLY* 4.2 10.3 - - - -
318A THR* 2.9 26.4 + - - +
321A ILE* 3.5 28.7 - - + +
401A GOL 2.6 42.0 + - - -
402A GOL 4.7 16.9 - - - -
1014B PRO 2.8 18.2 + - - +
1015B GLN* 3.6 7.4 - - - +
1016B VAL 3.1 0.2 - - - -
1017B TRP* 1.3 76.3 - - - +
1019B HIS* 1.3 66.8 + + + +
1021B LEU* 3.7 4.7 - - - +
1022B GLY* 3.3 18.2 + - - -
1025B ASN* 4.4 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1019 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.5 18.4 - - + +
26A SER 3.4 17.2 + - - -
29A LEU* 4.1 8.3 - - + -
77A LEU* 3.2 56.9 + - + +
79A TYR* 2.7 30.8 + + + +
103A LEU* 4.6 4.3 - - + -
402A GOL 4.1 18.8 - - - -
1015B GLN* 3.2 18.2 + - + -
1016B VAL 3.1 7.0 + - - +
1018B HIS* 1.3 82.8 - + + +
1020B PHE* 1.3 62.7 + - - +
1022B GLY 3.0 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1020 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 2.7 22.6 + - - +
29A LEU* 4.0 6.7 - - + -
115A ALA* 4.7 3.1 - - + -
118A LEU* 3.9 15.9 - - + -
119A THR* 3.1 48.2 - - + -
122A SER* 3.2 30.7 - - - -
123A VAL* 3.4 20.2 - - + +
403A N7I 3.3 15.0 - - - -
1016B VAL* 2.9 32.4 + - + -
1017B TRP* 3.4 38.4 - + - -
1019B HIS* 1.3 74.4 - - - +
1021B LEU* 1.3 70.2 + - + +
1022B GLY 3.2 0.4 - - - -
1023B TYR* 3.5 5.4 - - - -
----------------------------------------------------------
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