Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 3NMV
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
----------------------------------------------------------
14A GLU* 1.3 60.1 + - - +
15A GLN* 4.2 5.9 + - - +
16A LYS* 4.1 40.0 - - - +
17A THR* 2.5 32.5 + - - -
133A PHE* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 1.3 73.9 + - - +
15A GLN* 1.3 57.8 + - - +
17A THR* 3.1 6.9 + - - -
18A LEU* 2.8 48.0 + - + +
42A ARG* 2.7 35.1 + - - -
133A PHE* 3.6 27.6 - - + -
142A TYR* 2.6 39.2 + - - +
144A VAL* 3.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.2 5.3 + - - +
14A GLU* 1.3 82.6 + - - +
16A LYS* 1.3 65.7 + - + +
18A LEU* 3.2 8.4 + - + +
19A GLU* 3.0 48.1 + - + +
22A ILE* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.0 30.4 + - - +
14A GLU 3.1 0.8 - - - -
15A GLN* 1.3 84.1 - - + +
17A THR* 1.3 60.7 + - - +
19A GLU* 3.4 17.6 + - - +
20A PRO* 3.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 2.5 25.6 + - - -
14A GLU 3.4 6.5 - - - -
16A LYS* 1.3 77.0 - - - +
18A LEU* 1.3 61.3 + - - +
20A PRO* 3.3 13.4 - - - +
21A VAL* 3.7 13.1 - - + +
131A ASN* 5.2 9.4 - - - +
132A GLU 6.0 0.2 - - - +
133A PHE* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.8 43.1 + - + +
15A GLN* 3.2 8.2 + - + +
17A THR* 1.3 73.9 - - - +
19A GLU* 1.3 63.4 + - - +
20A PRO 3.5 0.4 - - - -
21A VAL* 3.1 7.5 + - + +
22A ILE* 3.0 36.4 + - + +
40A THR* 5.9 0.7 - - + -
42A ARG* 5.5 0.2 - - - +
131A ASN* 4.0 26.9 - - + +
133A PHE* 3.8 17.3 - - + -
144A VAL* 3.8 28.3 - - + +
146A LEU* 4.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.0 47.0 + - + +
16A LYS* 3.8 16.6 - - - +
18A LEU* 1.3 76.2 - - - +
20A PRO* 1.3 66.6 - - + +
22A ILE* 3.4 9.0 + - + +
23A LYS* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 3.3 13.9 - - - +
17A THR* 3.3 12.8 - - - +
19A GLU* 1.3 95.8 - - + +
21A VAL* 1.3 54.4 + - + +
23A LYS* 3.8 6.5 - - + +
24A THR* 2.7 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.7 16.8 - - + +
18A LEU* 3.1 13.2 + - + +
20A PRO* 1.3 76.6 - - + +
22A ILE* 1.3 54.2 + - - +
24A THR* 3.2 1.5 + - - -
25A TYR* 2.8 56.0 + - + +
26A HIS* 4.2 4.9 - - + -
109A VAL* 5.6 0.4 - - + -
129A SER* 3.4 31.9 - - - +
131A ASN* 3.8 31.0 - - - +
146A LEU* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 6.6 0.2 - - + -
18A LEU* 3.0 26.6 + - + +
19A GLU* 3.7 7.4 - - + +
21A VAL* 1.3 77.1 - - - +
23A LYS* 1.3 58.6 + - - +
26A HIS* 2.9 47.2 + - + +
27A GLN* 3.5 15.7 + - - +
38A LEU* 4.2 21.8 - - + -
146A LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 2.9 19.2 + - - +
20A PRO* 3.8 7.9 - - + +
22A ILE* 1.3 79.3 - - - +
24A THR* 1.3 64.0 + - - +
27A GLN* 3.8 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 2.7 27.5 + - - +
21A VAL 3.8 2.9 - - - -
23A LYS* 1.3 77.3 - - - +
25A TYR* 1.3 93.6 + - + +
27A GLN 5.2 0.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
21A VAL* 2.8 42.8 + - + +
24A THR* 1.3 99.0 - - + +
26A HIS* 1.3 70.4 + - + +
27A GLN 3.4 4.0 + - - -
28A PHE* 4.2 4.0 - - - -
102A PHE* 4.3 16.9 - + - -
104A ASP* 4.4 7.1 + - - -
107A HIS* 4.2 25.8 - + + +
109A VAL* 3.7 40.6 - - + -
127A VAL* 3.9 32.0 - - + +
129A SER* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL 3.9 15.0 - - - -
22A ILE* 2.9 33.4 + - + +
25A TYR* 1.3 82.2 + - + +
27A GLN* 1.3 62.1 + - - +
28A PHE* 4.2 7.8 - - - -
38A LEU* 4.5 12.5 - - + +
127A VAL* 3.6 21.3 - - + +
129A SER* 2.8 32.2 + - - -
146A LEU* 3.3 41.7 - - + +
148A SER* 2.8 32.0 + - - +
----------------------------------------------------------
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