Contacts of the strand formed by residues 104 - 115 (chain A) in PDB entry 4F8Q
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 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A LEU 3.0 31.2 - - - +
1A GLN* 3.6 28.3 - - - -
2A PHE* 3.6 44.0 - + - -
100A GLN* 3.3 5.6 - - - +
101A ASP 2.8 35.8 + - - +
103A ASP* 1.3 79.3 - - - +
105A TYR* 1.3 69.4 + - - +
106A GLU* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.9 34.3 - + + -
99A PHE 3.3 13.5 - - - +
100A GLN* 3.8 25.6 - - + +
103A ASP 4.7 7.9 - - - -
104A PHE* 1.3 87.8 - - - +
106A GLU* 1.3 76.6 + - - +
107A LYS* 5.1 11.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 3.3 29.1 - - + +
3A SER* 4.4 5.2 - - - -
4A VAL* 3.4 26.2 + - + +
98A TYR* 3.3 4.7 - - - +
99A PHE 3.1 29.4 + - - -
104A PHE* 4.1 9.3 - - + -
105A TYR* 1.3 87.2 - - - +
107A LYS* 1.3 78.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.8 9.4 - - - +
44A ARG* 4.5 11.9 - - - +
96A LEU* 4.5 16.2 - - + +
97A CYS 3.1 10.8 - - - +
98A TYR* 3.8 41.5 + - + +
105A TYR* 5.1 9.2 + - + -
106A GLU* 1.3 89.9 + - - +
108A ALA* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.2 26.0 - - + +
6A GLY* 3.3 24.9 - - - +
96A LEU* 3.3 8.3 - - - +
97A CYS* 2.9 48.4 + - - -
107A LYS* 1.3 72.5 - - - +
109A LEU* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY* 4.3 9.2 - - - +
7A PRO* 4.8 4.3 - - - +
41A SER* 4.1 7.6 - - - +
94A LYS* 3.6 36.3 - - + -
95A TYR 3.3 15.0 - - - +
96A LEU* 3.8 19.3 - - + -
108A ALA* 1.3 75.0 - - - +
110A VAL* 1.3 65.6 + - - +
111A GLU* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY* 4.4 0.2 - - - -
7A PRO* 3.7 28.7 - - + -
11A ILE* 4.0 6.1 - - + -
21A LEU* 3.9 41.1 - - + -
22A PRO 3.7 6.5 - - - +
23A CYS* 3.4 33.4 - - - -
38A TRP* 5.1 2.0 - - - +
94A LYS* 3.5 3.8 - - - +
95A TYR* 2.8 39.0 + - + +
97A CYS* 4.4 3.8 - - + -
109A LEU* 1.3 81.3 - - - +
111A GLU* 1.3 64.5 + - - +
112A LEU 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 5.5 0.4 - - - +
10A PRO* 3.6 26.0 - - + +
11A ILE* 2.7 37.2 + - - +
21A LEU* 4.7 0.4 - - - -
93A GLY* 3.7 13.4 - - - +
94A LYS* 4.5 23.6 + - + +
109A LEU* 5.9 2.2 - - + -
110A VAL* 1.3 80.4 - - - +
112A LEU* 1.3 64.0 + - - +
113A LYS* 3.3 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 14.8 - - + +
13A ALA* 4.1 9.2 - - + -
19A ALA* 3.8 23.8 - - + -
21A LEU* 4.2 10.3 - - + -
84A ILE* 4.3 12.6 - - + -
87A VAL* 4.5 6.3 - - + -
91A ASP* 3.5 31.0 - - + +
92A SER* 3.3 2.9 + - - -
93A GLY* 2.9 37.7 + - - +
95A TYR* 4.0 14.5 - - + -
110A VAL 4.2 0.4 + - - -
111A GLU* 1.3 76.8 - - - +
113A LYS* 1.3 64.6 + - - +
114A VAL* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.7 28.7 - - + -
11A ILE 2.8 10.5 + - - +
12A LEU* 3.5 27.9 - - + +
13A ALA 3.0 24.8 + - - +
92A SER* 3.7 4.5 - - - +
111A GLU* 3.3 22.5 + - + +
112A LEU* 1.3 76.7 - - - +
114A VAL* 1.3 62.6 + - - +
115A ALA* 4.1 0.7 + - - +
197A LEU* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.3 4.0 - - - +
15A VAL* 3.6 27.4 - - + +
87A VAL* 3.3 38.1 - - + -
88A THR 3.7 8.7 - - - +
89A ALA* 4.3 2.9 - - - +
92A SER* 3.4 25.6 + - - +
112A LEU* 3.6 29.6 - - + -
113A LYS* 1.3 73.7 - - - +
115A ALA* 1.3 61.0 + - - +
143A TYR* 2.9 25.9 - - + -
144A PRO* 3.9 8.0 - - - +
197A LEU* 4.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 2.9 5.1 + - - -
14A MET* 3.4 17.6 - - + +
15A VAL* 2.9 27.5 + - - -
113A LYS 4.1 0.4 + - - +
114A VAL* 1.3 74.9 - - - +
116A ALA* 1.3 60.6 + - - +
143A TYR 3.2 6.5 - - - +
144A PRO* 4.8 2.5 - - + -
195A ASN* 3.8 11.7 - - - +
197A LEU* 4.8 4.0 - - + -
198A LEU* 3.4 37.7 - - + -
----------------------------------------------------------
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