Contacts of the strand formed by residues 16 - 22 (chain H) 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 PHE 16 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H VAL* 2.9 9.2 - - - +
15H LYS* 1.3 93.2 - - + +
17H VAL* 1.3 63.6 + - - +
32H THR* 3.6 22.7 - - + -
33H ILE 3.5 2.9 - - - -
34H PRO* 3.9 20.9 - - + -
35H ALA 3.8 1.1 - - - +
82H ASP* 4.0 7.6 - - + -
83H SER 3.1 4.2 + - - -
84H THR* 3.0 3.5 - - - -
85H LEU 2.8 23.2 + - - -
1490H MPD 2.9 33.2 - - + -
193I SER* 3.5 32.3 - - - -
196I CYS* 3.8 20.0 - - + -
197I LEU* 3.4 34.3 - - + -
209I HIS* 4.3 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU* 4.1 20.9 - - + -
16H PHE* 1.3 79.5 - - - +
18H ASP* 1.3 61.9 + - - +
19H LEU* 3.5 26.7 + - + -
32H THR* 3.4 4.3 - - - -
33H ILE* 2.7 47.3 + - + +
35H ALA* 4.4 6.1 - - - -
38H VAL* 3.7 26.5 - - + -
42H PHE* 5.1 0.9 - - + -
85H LEU* 3.1 16.2 - - + +
87H ILE* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H VAL* 1.3 70.9 - - - +
19H LEU* 1.3 66.2 + - - +
20H ARG* 2.7 35.6 + - - +
30H HIS* 2.8 29.0 - - - +
31H VAL 3.5 4.4 - - - +
32H THR* 2.6 27.9 + - + +
80H PHE* 3.9 8.5 - - + -
84H THR* 4.0 14.9 + - - +
85H LEU 2.7 11.3 + - - +
86H ILE* 3.4 13.6 - - + +
87H ILE 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H VAL* 3.5 26.9 + - + -
18H ASP* 1.3 70.3 - - - +
20H ARG* 1.3 59.2 + - - +
21H PHE* 4.7 3.5 - - - -
29H GLN 4.4 0.2 - - - -
30H HIS* 3.1 6.6 - - - -
31H VAL* 2.8 55.3 + - + +
33H ILE* 4.4 25.8 - - + -
42H PHE* 4.1 28.3 - - + -
47H LYS* 5.2 7.4 - - + -
67H LEU* 4.5 13.5 - - + -
87H ILE* 3.5 14.1 - - + +
89H CYS* 3.8 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASP* 2.7 26.7 + - - +
19H LEU* 1.3 79.9 - - - +
21H PHE* 1.3 63.2 + - - +
28H GLU* 3.1 30.9 + - + +
29H GLN 3.2 11.0 - - - +
30H HIS* 3.8 1.3 - - + -
77H ASP* 2.9 24.0 + - - -
80H PHE* 3.4 10.1 - - - -
86H ILE* 3.5 42.3 - - + +
87H ILE 3.0 8.8 + - - +
88H ARG* 3.3 14.1 - - - +
89H CYS* 2.7 32.6 + - - -
202H MET* 5.1 0.6 - - - +
240H TYR* 3.4 37.6 + - - +
182I VAL* 4.1 9.9 - - - +
183I PRO* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU 4.7 2.9 - - - -
20H ARG* 1.3 79.3 - - - +
22H THR* 1.3 63.9 + - - +
23H ASP* 5.0 0.9 - - - -
28H GLU* 3.3 5.3 - - - +
29H GLN* 2.5 69.1 + - + +
30H HIS* 4.7 2.7 - - - -
31H VAL* 5.2 1.6 - - + -
49H PHE* 4.3 16.6 - + - -
54H ILE* 4.5 8.5 - - + -
57H TRP* 3.7 36.1 - + - -
67H LEU* 3.7 29.4 - - + -
88H ARG* 5.2 5.6 - - - +
89H CYS 4.0 15.3 - - - +
91H ILE* 3.9 13.9 - - + -
103H ASP* 6.0 0.9 - - - +
180I PHE* 4.1 21.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PHE* 1.3 80.7 - - - +
23H ASP* 1.3 76.1 + - - +
26H GLY* 3.5 27.8 - - - -
27H LYS 3.6 2.7 - - - -
28H GLU* 4.3 1.6 - - - +
57H TRP* 3.6 9.0 - - - -
88H ARG* 4.9 1.7 + - - -
103H ASP* 4.7 2.8 + - - +
104H PRO* 3.6 18.7 - - + +
105H ARG* 5.9 3.0 - - - +
236H GLN* 2.8 25.3 + - - +
366H ASN* 4.1 6.5 - - - +
368H TYR* 3.4 30.6 + - + -
----------------------------------------------------------
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