Contacts of the strand formed by residues 84 - 92 (chain I) in PDB entry 1F1H
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 THR 84 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I VAL* 4.1 0.7 - - - -
16I PHE* 3.0 13.0 + - - +
18I ASP* 4.0 17.0 + - - +
32I THR* 5.5 0.2 - - - +
76I ILE* 3.6 10.8 - - - +
77I ASP* 3.0 32.4 + - + +
80I PHE* 3.4 26.5 - - + -
82I ASP 2.6 30.7 + - - +
83I SER* 1.3 73.4 + - - +
85I LEU* 1.3 60.2 + - - +
1491I MPD 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I VAL* 4.0 21.3 - - + -
8I MET* 4.1 26.0 - - + -
9I LEU* 3.8 22.2 - - + -
14I VAL* 3.8 16.3 - - + +
16I PHE 2.8 8.6 + - - +
17I VAL* 3.1 11.1 - - + +
18I ASP 2.7 28.7 + - - -
74I ALA* 4.2 8.1 - - + -
75I VAL* 3.6 30.5 - - - +
76I ILE* 3.8 14.6 - - + +
84I THR* 1.3 73.4 - - - +
86I ILE* 1.3 63.7 + - - +
87I ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASP* 3.4 11.2 - - + +
20I ARG* 3.5 59.2 - - + +
73I THR 3.9 1.9 - - - +
74I ALA* 3.3 1.7 - - - -
75I VAL* 2.6 46.6 + - + +
77I ASP* 3.5 31.2 - - + +
84I THR* 5.1 0.2 - - - +
85I LEU* 1.3 73.2 - - - +
87I ILE* 1.3 72.5 + - - +
88I ARG* 4.7 9.4 - - - +
202I MET* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I VAL* 4.2 26.5 - - + -
17I VAL* 3.9 23.3 - - + -
18I ASP 2.9 9.0 + - - +
19I LEU* 3.5 12.4 - - + -
20I ARG 3.0 20.6 + - - -
38I VAL* 5.7 0.7 - - + -
42I PHE* 4.8 7.6 - - + -
43I PHE* 4.6 10.3 - - + -
69I PRO* 3.9 20.4 - - + -
70I ASP 3.7 17.5 - - - +
71I ALA* 4.7 2.2 - - - +
73I THR* 3.9 3.1 - - - +
74I ALA* 4.2 11.2 - - + +
85I LEU* 3.9 7.8 + - + -
86I ILE* 1.3 81.9 - - - +
88I ARG* 1.3 74.1 + - - +
89I CYS* 3.7 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ARG* 3.3 22.2 + - - +
21I PHE* 5.1 2.5 - - - +
22I THR* 4.9 3.4 + - - -
28I GLU* 2.5 46.2 + - - +
70I ASP* 3.0 25.6 + - - +
73I THR* 2.9 29.8 + - + +
75I VAL* 6.2 1.0 - - - +
86I ILE* 4.7 10.9 - - - +
87I ILE* 1.3 74.2 - - - +
89I CYS* 1.3 64.2 + - - +
105I ARG* 3.8 18.4 - - - +
233I ASP* 3.4 34.5 + - - +
236I GLN* 3.7 14.9 - - - +
237I ILE* 3.8 29.5 - - - +
368I TYR* 3.8 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 3.8 26.7 - - - -
20I ARG 2.7 15.9 + - - +
21I PHE* 4.0 10.0 - - - +
67I LEU* 3.6 31.4 - - + -
68I MET 3.3 10.3 - - - +
69I PRO* 3.8 19.3 - - - -
70I ASP* 4.4 0.4 - - - +
87I ILE 3.7 12.1 - - - -
88I ARG* 1.3 80.0 - - - +
90I ASP* 1.3 64.9 + - - +
103I ASP* 5.6 0.2 - - - +
105I ARG* 3.8 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I VAL 3.4 1.7 - - - +
67I LEU* 3.7 2.6 - - - -
68I MET* 2.8 45.8 + - + +
70I ASP* 4.3 5.0 - - - +
89I CYS* 1.3 73.7 - - - +
91I ILE* 1.3 62.9 + - - +
92I LEU* 3.9 17.9 - - + -
103I ASP* 3.7 8.3 - - - +
105I ARG* 3.0 40.6 + - - +
106I SER* 4.4 4.5 + - - +
109I LYS* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I PHE* 3.9 23.6 - - + -
49I PHE* 4.0 16.4 - - + -
57I TRP* 3.7 24.2 - - + -
65I MET* 3.7 31.9 - - + -
66I VAL 3.4 2.0 - - - +
67I LEU* 3.6 29.6 - - + -
90I ASP* 1.3 71.8 - - - +
92I LEU* 1.3 61.9 + - - +
99I GLY* 3.7 3.3 - - - -
100I TYR* 3.0 33.5 + - + +
103I ASP* 2.8 32.4 + - + +
106I SER* 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I MET* 3.4 7.5 - - - +
66I VAL* 2.9 39.7 + - + +
68I MET* 3.3 50.7 - - + -
90I ASP* 4.1 15.7 - - + +
91I ILE* 1.3 78.3 - - - +
93I GLU* 1.3 62.2 + - - +
97I LEU* 3.8 30.5 - - + +
98I GLN 4.1 5.2 - - - +
99I GLY* 3.5 24.7 - - - +
100I TYR 4.4 0.7 - - - -
106I SER* 4.6 2.0 - - - +
----------------------------------------------------------
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