Contacts of the helix formed by residues 99 - 108 (chain A) in PDB entry 5IZL
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 LEU 99 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 5.3 0.2 - - + -
48A THR 3.5 24.5 - - - +
49A LEU* 3.6 33.7 - - + +
94A PRO* 3.6 16.8 - - + -
96A HIS* 3.3 27.1 + - + +
97A ALA 3.1 2.0 - - - -
98A SER* 1.3 76.8 - - - +
100A ILE* 1.3 64.4 + - - +
101A ARG* 3.1 5.6 - - - -
102A THR* 3.1 27.0 + - - +
103A ILE* 3.5 7.3 + - - +
96B HIS* 4.3 8.1 - - + +
98B SER* 4.1 4.5 - - - +
437B ILE* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS 4.2 0.6 + - - +
97A ALA 3.6 11.3 + - - +
98A SER 3.5 2.0 - - - +
99A LEU* 1.3 77.6 - - - +
101A ARG* 1.3 67.7 + - - +
102A THR 3.0 1.4 + - - -
103A ILE* 3.1 38.6 + - + +
104A ILE* 3.1 21.3 + - + +
126A GLN* 4.6 7.6 - - + -
129A GLU* 3.7 35.4 - - + +
130A CYS* 5.1 1.8 - - - -
133A ILE* 4.4 13.9 - - + -
433A LEU* 3.5 40.6 - - + -
443A ARG* 4.2 3.1 - - - +
444A LEU* 5.2 7.4 - - + -
436B ASP* 5.0 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER 5.4 0.4 - - - +
99A LEU* 3.1 6.0 - - - +
100A ILE* 1.3 83.1 - - + +
102A THR* 1.3 65.3 + - - +
104A ILE* 4.1 11.6 - - - +
105A GLY* 3.7 12.6 + - - -
336A HIS* 4.6 10.5 - - - -
338A THR* 5.8 0.5 - - - +
343A THR* 2.6 59.0 + - + +
433A LEU* 5.3 4.5 - - + -
436B ASP* 2.4 41.9 + - - +
437B ILE* 5.4 1.9 - - + +
438B HIS* 3.3 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU 4.9 1.4 + - - -
50A ASP* 4.0 17.8 + - - +
51A LEU* 3.7 29.6 - - + +
94A PRO* 3.8 17.3 - - + -
99A LEU* 3.1 20.3 + - - +
100A ILE 3.0 0.4 - - - -
101A ARG* 1.3 81.8 - - - +
103A ILE* 1.3 60.5 + - - +
104A ILE 3.1 1.6 - - - -
105A GLY* 3.0 4.1 + - - +
106A GLY* 2.8 26.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
13A LEU* 3.7 32.4 - - + +
93A CYS* 4.3 13.1 - - + -
94A PRO* 3.2 37.9 - - + +
95A GLY* 4.5 7.9 - - - +
96A HIS 4.6 5.6 - - - +
99A LEU 3.7 10.5 - - - +
100A ILE* 3.1 32.3 + - + +
102A THR* 1.3 75.9 - - - +
104A ILE* 1.3 62.1 + - - +
106A GLY* 3.3 1.2 + - - -
107A ALA* 3.2 22.2 + - - +
126A GLN* 5.3 1.6 - - + -
130A CYS* 4.0 17.7 - - - -
133A ILE* 4.0 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.1 21.1 + - + +
101A ARG* 4.1 10.1 - - - +
102A THR 3.1 0.4 - - - -
103A ILE* 1.3 76.4 - - - +
105A GLY* 1.3 63.2 + - - +
107A ALA* 3.1 12.8 + - - +
108A GLN* 3.4 21.2 + - + +
133A ILE* 3.7 28.9 - - + -
338A THR* 4.0 36.8 - - + +
427A LEU* 6.0 0.2 - - + -
429A ILE* 4.3 24.9 - - + -
431A SER* 5.1 2.0 - - - +
433A LEU* 6.2 1.8 - - + -
444A LEU* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.8 2.2 - - - -
101A ARG 3.7 6.9 + - - -
102A THR* 3.0 10.0 + - - -
104A ILE* 1.3 80.7 - - - +
106A GLY* 1.3 61.0 + - - +
108A GLN* 3.4 16.1 + - - +
109A ILE* 3.3 21.2 - - - +
338A THR* 6.4 0.4 - - - -
341A HIS* 4.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.8 29.7 - - - +
91A VAL* 4.5 2.8 - - - +
93A CYS* 4.5 7.9 - - - -
102A THR 2.8 12.4 + - - -
103A ILE 3.3 3.8 + - - -
104A ILE 3.2 0.2 - - - -
105A GLY* 1.3 74.2 - - - +
107A ALA* 1.3 62.1 + - - +
109A ILE* 3.3 9.8 + - - +
110A ILE* 3.3 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.0 6.3 - - + +
103A ILE 3.2 7.7 + - - +
104A ILE 3.1 8.1 + - - +
106A GLY* 1.3 75.2 - - - +
108A GLN* 1.3 60.7 + - - +
109A ILE 3.1 4.0 + - - -
110A ILE* 3.7 26.9 + - + +
113A MET* 5.7 1.3 - - - -
133A ILE* 3.6 31.9 - - + +
137A ALA* 3.7 19.3 - - + +
138A CYS* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.4 21.0 + - + +
105A GLY* 3.4 5.1 + - - +
106A GLY 3.2 1.2 - - - -
107A ALA* 1.3 78.6 - - + +
109A ILE* 1.3 59.9 + - - +
110A ILE 3.6 2.0 - - - -
137A ALA* 5.0 8.1 - - + -
246A LEU* 3.5 18.8 - - - +
338A THR* 4.4 6.3 - - - +
340A GLY* 2.3 38.8 + - - -
341A HIS* 3.3 29.9 + - + +
427A LEU* 3.9 31.5 - - - +
----------------------------------------------------------
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