Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 1SSF
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 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 4.9 0.3 - - - +
17A LYS* 4.7 6.4 - - - +
19A SER 5.3 3.1 - - - +
21A ASN* 3.6 16.2 + - + +
22A GLY* 1.4 77.1 + - - +
24A PHE* 1.4 63.4 + - - +
25A TYR* 4.2 26.4 - + - -
68A THR* 5.9 0.4 - - + -
73A ASP* 2.6 34.5 + - - -
74A GLU* 3.9 12.7 - - - +
76A PHE* 3.4 32.5 - + + -
110A ILE* 4.2 8.3 - - + -
111A LEU 3.0 21.1 - - - +
112A SER* 4.0 7.6 - - - +
113A LEU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.8 16.8 - - + -
16A ALA 3.5 14.8 - - - +
17A LYS* 3.2 40.4 - - + -
23A TYR* 1.4 75.9 - - - +
25A TYR* 1.3 64.5 + - - +
110A ILE* 2.9 27.5 - - - +
111A LEU* 2.9 47.2 + - + +
112A SER 3.5 19.1 - - - -
113A LEU* 3.6 34.1 - - + -
116A GLY* 3.9 9.6 - - - -
125A LEU* 3.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.4 10.0 - - - +
16A ALA* 2.8 38.7 + - + +
17A LYS* 6.0 0.2 - - - -
23A TYR* 4.2 28.6 - + - -
24A PHE* 1.3 76.9 - - - +
26A SER* 1.3 61.2 + - - +
42A PHE* 4.9 8.1 - - + -
70A LEU* 4.8 10.4 - - + +
73A ASP* 4.9 6.8 + - - -
76A PHE* 4.6 7.6 - - - -
107A MET* 5.3 10.5 - - + -
109A VAL 5.2 5.8 - - - -
110A ILE* 3.9 28.7 - - + +
111A LEU* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL 3.7 5.7 + - - -
15A VAL* 5.3 0.9 - - - -
16A ALA* 3.8 4.6 - - - +
25A TYR* 1.3 76.1 - - - +
27A GLY* 1.4 56.4 + - - +
42A PHE* 3.4 22.5 - - - -
43A ASP* 3.2 27.3 + - - +
44A ASP* 4.5 0.2 - - - +
60A PRO* 6.2 0.9 - - - -
106A ARG* 3.0 58.3 + - - +
107A MET* 4.1 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.8 43.9 + - - +
15A VAL 4.2 0.6 - - - +
16A ALA* 4.3 4.2 - - - +
26A SER* 1.4 73.0 + - - +
28A LYS* 1.4 59.1 + - - -
41A LEU 4.0 0.7 - - - -
42A PHE* 4.0 15.3 - - - -
43A ASP* 4.0 3.8 - - - -
55A ILE* 4.8 3.1 - - - -
106A ARG* 3.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 3.8 5.6 - - - +
14A VAL* 3.4 7.7 - - - +
27A GLY* 1.4 72.8 - - - +
29A ILE* 1.4 64.7 + - - +
40A LEU* 3.7 0.5 - - - -
41A LEU* 2.8 71.0 + - + +
42A PHE 3.9 9.2 - - - +
43A ASP* 4.2 19.5 + - + +
45A GLY 5.6 0.2 - - - +
86A LYS* 3.7 39.0 - - - +
89A GLY* 5.5 9.3 - - - -
91A LEU* 5.7 0.9 - - + +
106A ARG* 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE 3.3 18.6 - - - +
10A VAL* 3.6 7.9 - - - +
11A GLY* 3.6 17.5 - - - +
12A LEU* 2.8 43.0 + - + +
14A VAL* 3.3 31.8 - - + +
28A LYS* 1.4 74.0 - - - +
30A THR* 1.4 60.3 + - - +
31A ARG 3.4 23.1 - - - +
32A ASP* 4.3 3.1 - - - +
38A TYR* 3.8 26.0 - - + -
39A LYS 3.3 7.6 - - - +
40A LEU* 3.8 11.0 - - + +
86A LYS* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.1 14.1 - - - +
11A GLY* 5.2 0.4 - - - -
28A LYS 4.6 0.2 + - - -
29A ILE* 1.4 71.7 + - - +
31A ARG* 1.4 73.5 + - + +
39A LYS* 2.8 24.0 + - - +
41A LEU* 4.1 13.3 + - - +
47A GLU* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.3 11.8 + - + -
29A ILE* 3.4 11.0 - - - +
30A THR* 1.4 90.3 - - + +
32A ASP* 1.4 64.3 + - - +
33A VAL* 6.0 0.4 - - + -
39A LYS* 3.0 57.8 + - + +
----------------------------------------------------------
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