Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 1IUF
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 TYR 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 4.3 1.9 - - - +
78A LYS* 1.3 89.2 - - + +
80A PRO* 1.3 66.2 - - + +
81A LEU* 3.6 5.8 - - + -
82A LEU* 3.2 52.3 - - + +
83A GLU* 3.0 30.3 + - - +
126A PHE* 5.3 8.5 - - + -
130A TRP* 4.0 30.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 5.7 8.7 - - + -
78A LYS 3.5 11.4 - - - +
79A TYR* 1.3 88.0 - - + +
81A LEU* 1.3 75.7 + - + +
83A GLU* 4.0 8.8 - - - +
84A ALA* 3.6 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 5.7 4.0 - - + -
80A PRO* 1.3 87.7 - - + +
82A LEU* 1.3 69.8 + - + +
84A ALA* 3.4 7.0 + - - +
85A ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.2 60.1 + - + +
80A PRO 3.4 0.2 - - - -
81A LEU* 1.3 82.2 - - + +
83A GLU* 1.3 51.6 + - - +
85A ALA* 3.3 2.4 + - + -
86A LEU* 2.5 78.5 + - + +
112A TRP* 5.0 2.0 - - + -
123A VAL* 5.5 1.8 - - + -
126A PHE* 3.8 24.7 - - + -
130A TRP* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 3.7 32.5 - - - +
79A TYR 3.0 23.5 + - - +
80A PRO* 4.0 8.7 - - - +
81A LEU 3.3 0.2 - - - -
82A LEU* 1.3 77.5 - - - +
84A ALA* 1.3 52.9 + - - +
86A LEU* 3.5 3.0 - - - -
87A PHE* 2.7 37.0 + - - +
130A TRP* 3.1 40.0 - - + +
133A GLY* 4.1 6.6 - - - -
134A PHE* 3.6 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO 3.6 10.5 + - - +
81A LEU* 3.4 9.8 + - - +
82A LEU 3.3 0.4 - - - -
83A GLU* 1.3 77.9 - - - +
85A ALA* 1.3 61.2 + - - +
87A PHE* 3.3 20.3 + - - +
88A GLU* 3.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 3.1 14.2 + - - +
82A LEU* 3.9 3.1 - - + +
84A ALA* 1.3 74.5 - - - +
86A LEU* 1.3 68.1 + - + +
87A PHE 3.0 4.7 - - - -
88A GLU* 2.7 37.9 - - - +
89A TRP* 3.6 5.4 + - - +
112A TRP* 5.7 1.1 - - + -
118A TYR* 4.6 7.3 + - + +
119A GLN* 4.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.5 57.5 + - + +
83A GLU* 3.5 2.7 - - - +
85A ALA* 1.3 75.8 - - + +
87A PHE* 1.3 63.4 + - - +
89A TRP* 2.6 48.4 + - + +
90A GLN 3.3 2.1 + - - -
108A ALA* 4.9 1.6 - - + -
112A TRP* 3.6 33.7 - - + -
126A PHE* 4.0 0.9 - - + -
130A TRP* 2.9 53.4 - - + -
131A LEU* 3.5 6.3 - - + +
134A PHE* 3.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 2.7 17.2 + - - +
84A ALA* 3.3 11.0 - - - +
86A LEU* 1.3 74.6 - - - +
88A GLU* 1.3 72.8 + - + +
89A TRP 2.6 6.1 + - - -
90A GLN* 2.5 27.5 + - - -
91A VAL* 2.9 37.0 + - + +
134A PHE* 3.2 38.4 - + + -
138A HIS* 5.3 7.2 - + + -
139A ILE* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.5 4.2 + - - +
85A ALA* 2.7 40.6 - - - +
87A PHE* 1.3 91.7 - - + +
89A TRP* 1.3 55.9 + - - +
91A VAL* 4.0 3.7 + - - +
92A GLN* 2.8 33.3 + - - +
118A TYR* 3.6 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA 4.2 4.3 - - - +
86A LEU* 2.6 47.9 - - + +
87A PHE 2.6 5.7 + - - -
88A GLU* 1.3 79.8 - - + +
90A GLN* 1.3 80.3 + - - -
92A GLN* 3.4 6.1 + - - +
93A GLN* 2.9 68.5 + - + +
103A THR 4.8 1.1 - - - -
104A ILE* 3.4 21.9 - - + +
107A ALA* 3.4 24.0 - - + -
108A ALA* 4.8 3.3 - - + +
111A LEU* 3.9 27.4 - - + -
118A TYR* 4.4 11.0 - - + +
131A LEU* 2.9 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 3.7 2.9 - - - +
87A PHE 2.5 13.2 + - - +
89A TRP* 1.3 113.4 - - - +
91A VAL* 1.3 54.7 + - - +
93A GLN 2.6 18.3 + - - +
94A GLY* 2.6 40.9 + - - +
97A ALA* 5.0 6.8 - - - +
103A THR* 6.0 1.6 - - - +
104A ILE* 4.0 3.4 - - - +
131A LEU* 3.3 24.0 - - + +
134A PHE* 3.6 17.7 - - + -
135A ARG* 4.1 23.7 + - + -
139A ILE* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.1 58.6 - - + +
88A GLU* 4.1 4.7 - - - +
90A GLN* 1.3 77.6 - - + +
92A GLN* 1.3 64.8 + - + +
94A GLY* 3.2 10.9 + - - -
95A ASP 5.0 0.5 + - - -
134A PHE* 5.6 0.2 - - + -
139A ILE* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 2.8 25.8 + - - +
89A TRP* 3.4 7.4 + - - +
90A GLN 3.1 0.4 - - - -
91A VAL* 1.3 78.2 - - + +
93A GLN* 1.3 62.2 + - + +
94A GLY 3.3 1.8 + - - -
95A ASP* 5.4 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 2.9 49.9 + - + +
90A GLN* 2.6 20.7 + - - +
92A GLN* 1.3 74.2 - - - +
94A GLY* 1.3 65.2 + - - +
95A ASP* 5.0 1.7 - - - +
97A ALA* 4.4 5.0 - - - +
107A ALA* 4.4 15.3 + - + +
110A ILE* 5.8 2.4 - - - +
111A LEU* 4.2 14.2 - - - +
----------------------------------------------------------
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