Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 1LEC
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 SER 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 2.8 25.1 + - - +
38A THR* 3.4 5.7 - - - +
39A LYS* 3.0 31.0 + - - +
47A VAL* 4.3 4.0 - - - -
48A ARG 3.6 5.6 - - - -
49A SER* 1.3 77.6 - - - +
51A ALA* 1.3 59.1 + - - +
105A TYR* 3.4 6.8 - - - +
220A GLY* 3.4 0.7 - - - -
221A VAL* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLY* 3.8 4.9 - - - -
27A ASP* 2.9 25.9 + - - +
37A LEU 4.0 3.1 - - - -
38A THR* 4.1 0.9 - - - -
50A SER* 1.3 75.5 + - - +
52A GLY* 1.3 58.6 + - - +
102A VAL* 3.8 19.4 - - + +
103A LYS 4.0 7.0 - - - +
105A TYR* 3.9 21.5 - - + +
110A GLY* 4.0 6.1 - - - -
219A ALA 3.3 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 3.3 11.7 - - - -
28A ALA* 3.7 3.8 - - - -
37A LEU* 3.0 26.6 + - - +
51A ALA* 1.3 76.7 - - - +
53A GLN* 1.3 67.7 + - - +
102A VAL* 4.1 2.7 - - - +
218A SER* 3.5 0.3 + - - -
219A ALA* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR 4.3 0.7 - - - -
24A PHE* 3.4 0.7 - - - -
25A LEU* 2.9 38.4 + - + +
28A ALA* 3.1 11.0 - - - +
37A LEU* 4.9 0.9 - - - -
52A GLY* 1.3 74.2 - - - +
54A ALA* 1.3 59.8 + - - +
55A SER 4.1 0.4 - - - -
94A PHE* 3.9 8.8 - - + -
101A SER 4.1 3.8 + - - -
102A VAL* 3.5 22.3 + - + +
110A GLY 3.1 25.7 + - - -
111A LEU* 3.8 10.9 - - - +
214A ARG* 2.7 47.3 + - - +
217A PHE 3.2 6.5 - - - +
218A SER* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.2 9.0 - - + -
23A THR 3.4 6.5 - - - -
24A PHE* 4.3 10.3 - - + +
28A ALA* 4.9 0.4 - - + -
35A LEU* 3.7 33.2 - - + -
37A LEU* 4.0 18.9 - - + +
53A GLN* 1.3 71.8 - - - +
55A SER* 1.3 59.4 + - - +
216A GLY* 3.2 1.6 - - - -
217A PHE* 2.8 35.8 + - + -
232A TRP* 4.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.3 7.0 - - - +
23A THR* 2.8 44.6 + - - +
25A LEU* 5.0 0.7 - - - +
53A GLN* 5.1 0.2 - - - +
54A ALA* 1.3 75.7 + - - +
56A TYR* 1.3 64.6 + - - +
94A PHE* 4.2 2.0 - - - -
214A ARG* 2.9 38.2 + - - -
215A ILE 3.0 19.3 - - - -
216A GLY* 3.7 4.9 - - - -
232A TRP* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.0 10.6 - - + +
6A PHE* 3.5 48.6 - + + +
8A TYR* 4.1 13.9 - - - -
21A GLU* 3.4 23.3 - - + -
22A ILE* 4.5 2.7 - - + +
23A THR* 5.4 0.3 - - - -
55A SER* 1.3 76.9 + - - +
57A SER* 1.3 64.4 + - - +
58A GLU* 3.5 62.7 + - + +
60A VAL* 4.4 10.5 - - + -
214A ARG* 4.8 9.2 - - - +
215A ILE* 2.9 21.8 + - + +
232A TRP* 3.8 22.1 - + + -
----------------------------------------------------------
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