Contacts of the helix formed by residues 89 - 105 (chain A) in PDB entry 1F1J
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 GLY 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 1.3 72.0 - - - +
90A THR* 1.3 62.7 + - - +
91A ASP 3.3 2.5 - - - -
92A LYS* 3.2 9.4 + - - +
93A ASP* 3.2 16.9 + - - -
233A ARG* 4.7 0.7 - - - -
235A PRO 3.2 18.3 + - - -
238A GLY* 3.5 21.4 - - - -
1201A SO4 2.7 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 2.7 30.1 + - - +
76A LYS* 3.5 28.7 - - + -
87A ARG* 2.8 55.5 + - - +
88A ASN 3.2 3.4 + - - -
89A GLY* 1.3 76.7 - - - +
91A ASP* 1.3 64.3 + - - +
93A ASP* 3.4 9.9 + - - +
94A ALA* 3.0 22.7 + - - +
142A LEU* 3.7 9.0 - - - +
233A ARG* 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 2.8 31.4 + - - +
76A LYS* 3.2 30.9 + - - +
90A THR* 1.3 73.6 - - - +
92A LYS* 1.3 60.6 + - - +
94A ALA* 3.4 1.8 + - - +
95A GLU* 2.9 30.7 + - - +
112A ASN* 4.2 4.3 - - - +
1201A SO4 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY* 3.2 8.5 + - - +
91A ASP* 1.3 73.8 - - - +
93A ASP* 1.3 67.1 + - - +
95A GLU* 3.3 7.4 + - - +
96A ALA* 3.0 25.2 + - - +
235A PRO 4.0 7.3 + - - -
236A GLY* 3.1 38.3 + - - +
237A ARG* 4.3 14.8 - - - +
238A GLY 4.8 0.2 - - - +
1201A SO4 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.7 3.8 + - - -
89A GLY 3.2 9.1 + - - +
90A THR* 3.5 13.9 + - - +
92A LYS* 1.3 80.1 - - - +
94A ALA* 1.3 53.2 + - - +
96A ALA* 3.1 3.9 + - - +
97A LEU* 2.7 39.2 + - - +
142A LEU* 4.0 11.3 - - + +
184A GLN* 5.0 0.9 - - - +
233A ARG* 4.7 2.4 - - - -
237A ARG 4.0 3.1 - - - +
238A GLY* 3.1 20.6 - - - -
239A SER* 2.8 38.4 + - - +
242A VAL* 3.6 23.7 - - + +
243A GLN* 4.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.2 7.3 - - + +
74A ASN* 3.7 27.1 - - + +
90A THR 3.0 14.4 + - - +
91A ASP 3.6 4.7 - - - +
93A ASP* 1.3 79.0 - - - +
95A GLU* 1.3 58.2 + - - +
97A LEU* 3.6 5.6 - - - +
98A PHE* 2.7 31.1 + - - +
110A VAL* 4.4 15.0 - - + +
142A LEU* 3.8 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP 2.9 18.0 + - - +
92A LYS* 3.8 6.7 - - - +
94A ALA* 1.3 76.0 - - - +
96A ALA* 1.3 57.4 + - - +
98A PHE* 3.2 10.0 + - + +
99A LYS* 2.8 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS 3.0 17.7 + - - +
93A ASP* 3.4 5.6 - - - +
95A GLU* 1.3 74.0 - - - +
97A LEU* 1.3 65.9 + - - +
99A LYS* 3.0 11.9 + - - +
100A CYS* 2.9 25.3 + - - -
242A VAL* 5.0 2.0 - - + -
246A CYS* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.1 13.1 - - + +
93A ASP 2.7 23.7 + - - +
94A ALA* 3.7 4.5 - - - +
96A ALA* 1.3 73.4 - - - +
98A PHE* 1.3 61.4 - - - +
100A CYS* 4.5 1.1 - - - +
101A PHE* 3.0 51.4 + - + +
140A ILE* 3.6 31.4 - - + -
142A LEU* 3.7 25.6 - - + -
242A VAL* 3.5 20.2 - - + -
245A LEU* 4.2 15.7 - - + -
246A CYS* 3.7 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.0 6.3 - - - +
94A ALA 2.7 21.7 + - - +
95A GLU* 3.2 11.9 - - + +
96A ALA 3.1 0.2 - - - -
97A LEU* 1.3 74.5 - - - +
99A LYS* 1.3 71.7 + - + +
102A ARG* 3.1 43.5 + - + +
108A VAL* 3.3 56.7 - - + +
109A ILE* 4.9 1.3 - - - -
110A VAL* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 2.8 55.6 + - + +
96A ALA* 3.0 8.9 + - - +
98A PHE* 1.3 85.5 - - + +
100A CYS* 1.3 57.0 + - - +
102A ARG* 3.6 5.5 - - - +
103A SER* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 2.9 12.6 + - - +
97A LEU 3.9 3.1 - - - +
99A LYS* 1.3 76.1 - - - +
101A PHE* 1.3 67.9 + - + +
103A SER* 2.9 11.5 + - - -
104A LEU* 2.8 29.8 + - - +
246A CYS* 3.5 51.8 - - - -
249A LEU* 4.4 16.6 - - + -
250A GLU* 4.6 10.3 - - - +
254A LYS* 5.3 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A CYS* 3.7 27.8 - - - -
97A LEU* 3.0 34.1 + - + +
98A PHE 4.6 0.7 - - - +
100A CYS* 1.3 82.4 - - + +
102A ARG* 1.3 59.9 + - - +
104A LEU* 3.3 12.4 + - + +
105A GLY 3.1 5.2 + - - -
106A PHE* 3.0 55.3 + + + +
108A VAL* 4.6 4.0 - - + -
138A ALA* 4.3 3.8 - - + -
140A ILE* 3.7 23.6 - - + -
180A LEU* 5.8 0.4 - - + -
182A PHE* 3.7 41.7 - + - -
245A LEU* 4.7 1.6 - - + -
249A LEU* 3.7 25.1 - - + -
301A PHE* 5.9 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.1 41.0 + - + +
99A LYS* 3.6 5.8 - - - +
101A PHE* 1.3 72.9 - - - +
103A SER* 1.3 59.9 + - - +
105A GLY* 2.6 37.9 + - - -
106A PHE 2.7 34.8 + - - -
107A ASP* 3.7 15.0 + - - +
108A VAL* 4.1 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 2.8 21.6 + - - +
100A CYS* 3.1 10.7 - - - -
102A ARG* 1.3 78.8 - - - +
104A LEU* 1.3 61.3 + - - +
105A GLY* 3.1 2.3 + - - -
254A LYS* 4.3 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.1 19.5 - - + +
100A CYS 2.8 16.8 + - - +
101A PHE* 3.4 21.1 - - + +
102A ARG 3.1 0.2 - - - -
103A SER* 1.3 75.2 - - - +
105A GLY* 1.3 57.7 + - - +
106A PHE* 4.0 22.4 - - + -
249A LEU* 4.3 19.5 - - + +
253A GLY* 3.9 11.7 - - - +
254A LYS* 3.7 32.6 - - + +
301A PHE* 3.8 49.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
67A LEU* 3.3 24.1 + - - +
68A GLY 4.5 0.2 + - - -
101A PHE 3.1 0.2 + - - -
102A ARG* 2.6 31.3 + - - -
103A SER 3.0 1.7 - - - -
104A LEU* 1.3 73.2 - - - +
106A PHE* 1.3 63.7 + - - +
107A ASP* 4.0 4.2 + - - +
----------------------------------------------------------
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