Contacts of the helix formed by residues 101 - 116 (chain A) in PDB entry 1B70
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 HIS 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 1.3 75.0 - - - +
102A PRO* 1.3 68.7 - - + +
103A ILE* 3.0 47.8 - - + +
104A THR* 2.8 32.8 + - - +
105A LEU* 3.0 10.4 + - - +
335A PHE* 3.1 36.5 + - - +
343A LEU* 3.6 25.6 - - + +
509B GLU* 3.2 30.0 + - + +
510B VAL 4.4 0.4 - - - -
511B TYR* 3.4 36.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU 3.5 5.6 - - - +
101A HIS* 1.3 101.7 - - + +
103A ILE* 1.3 53.6 + - - +
105A LEU* 3.2 13.0 + - + -
106A MET* 2.7 36.1 + - - +
323A ALA* 5.3 0.7 - - - -
327A TYR* 3.4 22.1 - - + -
329A ILE* 4.9 0.2 - - + -
335A PHE* 4.0 23.8 - - + -
342A PHE* 4.3 4.9 - - + -
343A LEU* 4.1 10.5 - - + +
346A PHE* 4.2 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A HIS* 3.0 27.8 - - + +
102A PRO* 1.3 76.0 - - - +
104A THR* 1.3 54.4 + - - +
106A MET* 3.2 3.2 + - - +
107A GLU* 2.6 46.7 + - + +
217A HIS* 4.1 22.4 - - + +
319A VAL* 3.9 23.2 - - + +
320A GLU* 3.8 38.6 - - + +
323A ALA* 4.7 4.7 - - + -
335A PHE* 4.1 15.3 - - + -
511B TYR* 3.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.8 12.8 - - + -
101A HIS* 2.8 12.8 + - - +
103A ILE* 1.3 78.5 - - - +
105A LEU* 1.3 51.2 + - - -
107A GLU* 3.5 8.3 - - + +
108A ARG* 2.7 38.3 + - + +
496B GLN* 4.0 23.3 + - - +
499B ARG* 4.2 15.0 - - + +
509B GLU* 2.7 25.9 + - - +
511B TYR* 2.5 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.6 38.4 - - + +
101A HIS 3.0 12.1 + - - +
102A PRO* 3.4 14.1 - - + +
104A THR* 1.3 75.9 - - - +
106A MET* 1.3 51.7 - - - +
108A ARG* 3.1 38.5 + - - +
109A GLU* 2.8 35.5 + - - +
327A TYR* 3.3 15.9 + - + +
346A PHE* 3.9 20.9 - - + +
347A LYS 5.9 1.1 - - - +
349A VAL* 3.4 28.3 - - + -
350A LEU* 4.2 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 2.7 20.8 + - - +
103A ILE 3.6 3.1 - - - +
105A LEU* 1.3 68.6 - - - +
107A GLU* 1.3 67.7 + - - +
109A GLU* 3.1 34.0 + - + +
110A LEU* 2.8 46.5 + - + +
244A LEU* 4.8 2.7 - - + -
319A VAL* 3.9 12.6 - - + +
322A LEU* 3.8 15.7 - - + -
323A ALA* 3.7 38.8 - - + +
326A ARG* 3.9 20.0 - - - -
327A TYR* 3.2 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 2.6 31.4 + - + +
104A THR* 3.5 7.5 - - - +
106A MET* 1.3 73.0 - - - +
108A ARG* 1.3 66.3 + - - +
110A LEU* 3.1 9.0 + - - +
111A VAL* 2.8 31.0 + - + +
123A GLU* 5.3 2.0 - - - +
199A PRO* 3.6 23.0 - - + +
200A GLY* 4.8 3.8 + - - -
217A HIS* 5.1 8.0 - - - +
319A VAL* 4.7 7.7 - - + +
492B TYR* 2.8 35.5 + - - +
496B GLN* 4.0 4.4 + - - +
499B ARG* 3.9 20.6 + - - -
511B TYR* 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.1 11.6 - - - +
104A THR* 2.7 25.0 + - + +
105A LEU* 3.2 27.6 + - - +
107A GLU* 1.3 73.5 - - - +
109A GLU* 1.3 59.9 + - - +
111A VAL* 3.1 8.7 + - - +
112A GLU* 2.8 41.3 + - + +
115A ARG* 6.2 1.3 - - - +
350A LEU* 3.3 42.8 + - - +
492B TYR* 5.4 1.3 - - - -
496B GLN* 5.9 5.2 - - - +
500B GLU* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 2.8 16.9 + - - +
106A MET* 3.4 22.7 - - + +
108A ARG* 1.3 75.1 - - - +
110A LEU* 1.3 64.0 + - - +
112A GLU* 3.2 6.9 + - - +
113A ILE* 3.0 31.1 + - + +
243A ALA 5.2 2.3 - - - +
244A LEU* 4.0 13.2 - - + +
326A ARG* 3.3 35.3 + - - -
327A TYR* 3.5 12.7 + - - +
350A LEU* 5.7 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 2.8 42.3 + - + +
107A GLU* 3.5 8.1 - - - +
109A GLU* 1.3 73.1 - - - +
111A VAL* 1.3 64.8 + - + +
113A ILE* 3.1 10.7 + - - +
114A PHE* 3.1 30.5 + - + -
219A LEU* 4.3 24.7 - - + -
240A LEU* 4.3 23.1 - - + -
244A LEU* 4.9 2.9 - - + -
317A LEU* 4.7 13.2 - - + -
319A VAL* 4.6 17.7 - - + -
322A LEU* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 2.8 23.2 + - + +
108A ARG* 3.4 9.4 - - - +
110A LEU* 1.3 73.9 - - - +
112A GLU* 1.3 68.1 + - - +
113A ILE 3.0 0.3 + - - -
114A PHE* 3.2 6.2 + - - +
115A ARG* 2.8 56.1 + - + +
121A ALA* 4.3 11.7 - - + -
197A VAL* 5.0 6.9 - - + +
199A PRO* 4.8 9.0 - - + -
219A LEU* 4.9 12.1 - - + -
492B TYR* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 2.8 29.9 + - + +
109A GLU* 3.7 7.0 - - - +
111A VAL* 1.3 73.2 - - - +
113A ILE* 1.3 65.3 + - + +
115A ARG* 3.3 34.0 + - - +
116A ALA* 3.3 18.0 + - - +
493B ARG* 5.2 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.0 22.3 + - + +
110A LEU* 3.2 11.0 - - - +
111A VAL 3.0 0.6 - - - -
112A GLU* 1.3 78.5 - - + +
114A PHE* 1.3 59.1 + - + +
116A ALA* 3.1 14.1 + - - +
117A LEU* 2.7 32.1 - - + +
239A GLU 5.5 0.2 - - - -
240A LEU* 4.1 23.8 - - + -
243A ALA* 3.1 47.1 - - + +
244A LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.1 26.6 + - + +
111A VAL 4.0 2.9 - - - +
113A ILE* 1.3 79.0 - - + +
115A ARG* 1.3 65.7 + - - +
117A LEU* 2.9 18.1 + - + -
119A TYR* 2.9 57.7 + + + -
197A VAL* 4.2 13.2 - - + -
219A LEU* 3.8 27.6 - - + -
236A ALA* 4.8 9.2 - - + -
237A ILE* 4.9 2.0 - - + -
240A LEU* 3.8 47.6 - - + -
315A PHE* 3.4 33.0 - + - -
317A LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 6.2 1.6 - - - +
111A VAL* 2.8 38.3 + - + +
112A GLU* 3.4 37.9 + - - +
114A PHE* 1.3 78.4 - - - +
116A ALA* 1.3 56.5 + - - +
117A LEU 3.0 0.2 - - - -
118A GLY* 2.9 20.4 + - - -
119A TYR 3.5 12.5 + - - +
489B GLU* 2.7 30.7 + - - +
492B TYR* 4.0 19.6 - - - -
493B ARG* 2.9 56.6 - - - +
496B GLN* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU 3.3 7.4 + - - +
113A ILE* 3.1 14.1 + - - +
115A ARG* 1.3 77.5 - - - +
117A LEU* 1.3 60.7 + - + +
118A GLY 3.3 1.3 + - - -
----------------------------------------------------------
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