Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 3T2D
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 ARG 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 1.3 78.4 - - - +
3A VAL* 1.3 60.2 + - - +
61A THR* 3.6 21.5 - - - +
117A GLU* 3.9 35.5 + - + +
118A PHE* 3.3 24.3 - - - +
119A GLU* 3.3 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.5 10.1 - - + -
2A ARG* 1.3 75.5 - - - +
4A THR* 1.3 73.6 + - - +
5A VAL* 4.7 0.9 - - + -
43A ILE* 4.9 0.7 - - + -
59A THR* 4.4 6.3 - - + -
60A HIS 3.6 17.3 - - - +
61A THR* 5.2 0.4 - - - +
116A MET 3.9 0.9 - - - +
117A GLU* 3.2 3.7 - - - -
118A PHE* 2.9 64.4 + - + +
120A GLU* 4.2 17.5 - - + +
309A LEU* 4.3 8.5 - - + -
312A GLY* 3.9 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 1.3 76.6 - - - +
5A VAL* 1.4 68.3 + - - +
6A SER* 3.7 9.2 - - - +
59A THR* 3.3 5.5 - - - -
60A HIS* 2.8 66.4 + - + +
61A THR* 4.7 1.2 - - - +
62A LYS 4.4 0.2 + - - -
63A GLY* 3.2 35.7 + - - +
64A GLU* 4.1 8.1 - - + +
115A GLU* 4.5 0.9 - - + +
116A MET 3.3 15.0 - - - +
117A GLU* 3.6 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.7 1.8 - - + -
4A THR* 1.4 78.1 - - - +
6A SER* 1.3 63.1 - - - +
57A LEU* 3.5 26.7 - - + -
58A MET 3.7 2.0 - - - -
59A THR* 4.1 13.0 - - + -
115A GLU* 3.1 4.2 - - - +
116A MET* 2.9 33.9 + - + +
118A PHE* 3.7 18.6 - - + -
126A ILE* 4.0 12.1 - - + -
238A LEU* 3.4 23.1 - - + +
309A LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.7 1.4 - - - +
5A VAL* 1.3 74.2 - - - +
7A ILE* 1.3 62.5 + - - +
8A ILE* 4.6 8.7 - - - -
56A LEU 3.4 3.1 - - - +
57A LEU* 3.5 2.1 - - - -
58A MET* 2.8 41.2 + - - +
60A HIS* 2.9 28.0 + - - -
69A ILE* 4.3 11.1 - - - +
114A ALA 3.6 4.7 - - - -
115A GLU* 2.7 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 1.3 70.8 - - - +
8A ILE* 1.3 66.0 + - - +
9A LYS 4.1 0.2 - - - -
48A TYR* 4.1 5.2 - - - +
55A SER* 3.8 31.6 - - - +
56A LEU 3.4 6.3 - - - +
57A LEU* 3.7 20.6 - - + -
112A GLN 3.7 0.7 - - - +
113A VAL* 3.3 5.5 - - - +
114A ALA* 2.8 38.7 + - + +
128A ALA* 3.9 12.8 - - + -
129A PHE 4.5 1.6 - - - +
236A VAL* 3.8 19.2 - - + +
237A LEU 3.7 25.1 - - - +
238A LEU* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 4.6 5.2 - - - -
7A ILE* 1.3 79.4 - - - +
9A LYS* 1.3 62.6 + - - +
56A LEU* 2.8 34.6 + - - +
58A MET* 3.9 17.9 - - + -
69A ILE* 4.0 5.4 - - + +
70A HIS* 3.8 47.6 - - + +
73A ALA* 3.5 27.8 - - + -
77A PHE* 3.5 6.4 - - + -
111A PRO* 3.9 20.2 - - + -
112A GLN 3.3 9.4 - - - +
113A VAL* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.7 0.2 - - + -
8A ILE* 1.3 75.2 - - - +
10A ALA* 1.3 77.3 + - - +
53A ASP* 3.1 36.0 + - + -
54A ILE 3.1 16.2 - - - +
55A SER* 3.8 9.4 - - - +
77A PHE* 3.7 2.2 - - - -
96A ASP* 4.1 9.5 + - - +
111A PRO* 3.1 5.7 - - - +
112A GLN* 2.9 47.3 + - + +
130A ALA* 6.0 0.4 - - + -
131A ALA 5.8 0.2 - - - +
233A ASP 3.1 17.4 + - - -
234A ASP* 3.1 30.1 + - - +
236A VAL* 3.7 29.4 - - + -
410A MG 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 1.3 83.3 - - - +
11A ASP* 1.3 61.1 + - - +
12A VAL* 4.0 3.9 + - + -
54A ILE* 2.9 36.1 + - - +
77A PHE* 3.4 33.8 - - + -
96A ASP* 3.6 17.7 - - + +
97A LEU* 4.4 7.9 - - + -
111A PRO* 4.2 9.9 - - + -
----------------------------------------------------------
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