Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 1V2E
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 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS 3.1 2.5 + - - -
12A GLU* 1.3 76.4 - - - +
14A ILE* 1.3 67.2 + - - +
15A PHE* 3.4 9.5 + - - -
16A PRO* 3.4 26.4 - - - +
17A ARG* 3.3 19.1 + - - +
113A ASP* 3.2 30.7 + - - -
249B GLN* 3.0 29.9 - - - +
250B TRP* 4.9 2.0 - - - -
253B PHE* 4.8 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.5 2.5 + - - -
13A SER* 1.3 74.5 + - - +
15A PHE* 1.3 88.5 + - + +
17A ARG* 3.2 16.2 + - - +
18A MET* 3.0 38.0 + - + +
113A ASP* 4.3 8.3 + - + +
320A PHE* 4.5 17.9 - - + -
331A ILE* 4.3 18.8 - - + -
332A PRO* 4.5 11.9 - - + -
335A ALA* 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.2 15.4 - - - -
14A ILE* 1.3 83.9 - - + +
16A PRO* 1.3 69.1 - - + +
18A MET* 3.5 2.4 + - - +
19A SER* 3.3 21.8 + - - -
32A GLN* 3.6 23.4 - - + +
112A PHE* 3.8 15.9 - + - -
113A ASP* 3.3 30.5 - - + -
331A ILE* 3.8 28.3 - - + -
336A PHE* 3.7 21.1 - + - -
347A ARG* 3.2 30.3 - - - -
520A KMT 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 4.2 10.8 - - + +
13A SER* 3.4 32.3 - - - +
15A PHE* 1.3 96.4 - - + +
17A ARG* 1.3 59.9 + - - +
19A SER* 3.4 3.5 + - - -
20A GLY* 3.3 16.8 + - - -
32A GLN* 4.0 12.8 - - - +
58B ALA 5.9 0.2 - - - +
59B PRO* 5.2 4.7 - - + -
60B PRO* 3.9 31.6 - - + -
249B GLN* 4.5 1.1 - - - +
253B PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 4.0 29.6 + - + +
13A SER 3.3 17.4 + - - +
14A ILE* 3.2 18.4 + - - +
15A PHE 3.2 1.0 - - - -
16A PRO* 1.3 79.2 - - - +
18A MET* 1.3 61.9 + - - +
20A GLY* 3.3 3.1 + - - -
21A LEU* 3.2 22.7 + - + +
320A PHE* 3.0 45.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.0 34.0 + - + +
15A PHE 4.1 3.4 - - - +
17A ARG* 1.3 74.4 - - + +
19A SER* 1.3 59.8 + - - +
21A LEU* 3.5 28.2 - - - +
22A ALA* 2.9 29.5 + - - +
29A ASN* 5.2 4.3 - - - +
31A GLY* 5.8 0.9 - - - -
32A GLN 5.8 0.7 - - - +
319A ALA* 4.5 13.5 - - + +
320A PHE* 4.4 11.9 - - + -
323A VAL* 4.5 9.2 - - + -
329A ALA* 3.6 19.8 - - + +
330A LEU 2.8 45.8 - - - +
331A ILE* 4.2 11.9 - - + -
332A PRO* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE 3.3 3.0 + - - -
16A PRO* 3.6 9.4 - - - -
17A ARG 3.2 0.8 - - - -
18A MET* 1.3 77.6 - - - +
20A GLY* 1.3 61.2 + - - +
22A ALA* 3.5 3.2 + - - +
23A GLN* 3.3 28.3 + - - +
29A ASN* 3.2 26.5 + - - +
32A GLN* 2.5 38.3 + - - +
34A PHE* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO 3.3 7.2 + - - -
17A ARG 3.3 6.3 + - - -
18A MET 3.2 0.4 - - - -
19A SER* 1.3 78.2 - - - +
21A LEU* 1.3 65.3 + - - +
22A ALA 3.1 0.2 - - - -
23A GLN* 3.4 13.1 + - - +
24A ARG* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.2 15.1 + - + +
18A MET* 3.5 21.3 - - - +
20A GLY* 1.3 78.2 - - - +
22A ALA* 1.3 56.3 + - - +
24A ARG* 3.4 35.9 - - - +
25A LEU* 3.0 53.9 + - + +
320A PHE* 3.7 33.9 - - + -
323A VAL* 3.7 19.7 - - + -
324A GLU* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET 2.9 16.6 + - - +
19A SER 3.7 6.3 - - - +
20A GLY 3.1 0.2 - - - -
21A LEU* 1.3 74.5 - - - +
23A GLN* 1.3 61.0 + - - +
25A LEU 3.2 0.7 + - - -
26A GLY* 2.8 25.3 + - - -
27A ALA* 3.0 30.3 + - + +
29A ASN* 4.3 15.0 - - + -
323A VAL* 4.5 2.4 - - - +
329A ALA* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.3 16.7 + - - +
20A GLY* 3.9 10.6 - - - +
22A ALA* 1.3 76.4 - - + +
24A ARG* 1.3 64.6 + - - +
26A GLY* 3.2 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY 3.1 13.6 + - - +
21A LEU* 3.4 34.2 - - - +
23A GLN* 1.3 82.7 - - - +
25A LEU* 1.3 66.5 + - + +
26A GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.0 31.5 + - + +
22A ALA 4.1 2.2 - - - +
23A GLN 3.2 0.2 - - - -
24A ARG* 1.3 83.3 - - + +
26A GLY* 1.3 60.0 + - - +
27A ALA* 4.3 4.9 - - + +
323A VAL* 3.5 47.6 - - + +
324A GLU* 3.8 28.0 - - + +
327A ARG* 3.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.8 6.2 + - - -
23A GLN* 3.2 10.8 + - - -
24A ARG 3.4 0.6 + - - -
25A LEU* 1.3 78.8 - - - +
27A ALA* 1.3 62.6 + - - +
327A ARG* 4.1 8.1 + - - -
363A ARG* 3.2 17.5 + - - -
----------------------------------------------------------
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