Contacts of the helix formed by residues 58 - 63 (chain B) in PDB entry 2X7N
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 ILE 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.1 33.7 - - + +
16B PHE* 4.4 9.2 - - + -
56B THR* 3.5 16.9 - - - +
57B ARG* 1.3 76.5 - - - +
59B ILE* 1.3 63.0 + - - +
60B GLY 3.0 1.6 + - - -
61B ARG* 3.1 19.2 + - + -
62B MET* 3.1 15.8 + - + +
113C VAL* 6.0 0.2 - - + -
115C LYS 5.3 1.1 - - - +
118C ALA* 3.8 38.6 - - + -
119C ASP* 4.4 5.8 - - + +
125C ALA* 4.3 10.8 - - + +
128C SER* 6.0 1.6 - - - -
131C VAL* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE 3.5 16.4 - - - +
17B SER* 4.0 4.0 - - - -
18B LYS* 4.1 3.1 - - + +
25B LEU* 3.3 52.5 - - + +
26B VAL* 3.6 6.5 - - - +
27B ALA* 4.0 3.8 - - - +
51B THR* 3.4 30.1 - - + +
52B THR* 4.0 5.2 - - - -
53B ILE* 3.9 25.6 - - + +
56B THR* 4.2 0.4 + - - +
57B ARG 3.0 14.6 + - - +
58B ILE* 1.3 74.6 - - - +
60B GLY* 1.3 61.2 + - - +
62B MET* 3.8 9.0 - - - -
63B THR* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.1 23.6 - - - -
15B VAL 2.9 8.1 + - - -
17B SER 3.4 18.2 - - - -
18B LYS* 3.2 27.4 + - - -
59B ILE* 1.3 81.4 - - - +
61B ARG* 1.3 64.8 + - - +
63B THR 3.3 6.1 - - - +
105B GLY* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 3.4 15.7 + - - -
15B VAL* 3.6 24.4 + - + -
18B LYS* 4.2 8.3 - - - +
58B ILE* 3.1 13.7 + - + +
60B GLY* 1.3 91.3 + - - +
62B MET* 1.3 57.2 + - - +
63B THR 3.3 0.9 - - - -
103B ALA* 3.0 18.8 - - + +
105B GLY* 2.7 45.8 + - - -
106B ASN* 2.8 26.2 - - - +
149B GLY 3.4 14.1 + - - -
150B SER* 3.9 6.7 - - - +
194B GLY 3.6 18.3 + - - -
195B ALA* 4.1 6.6 - - - +
125C ALA 4.1 9.4 - - - +
126C SER* 3.3 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.7 18.2 - - + +
54B ALA* 4.1 18.4 - - + -
56B THR* 3.6 9.2 - - - +
58B ILE* 3.1 32.4 + - + +
59B ILE 4.2 2.0 - - - +
60B GLY 3.4 0.2 - - - -
61B ARG* 1.3 78.4 - - - +
63B THR* 1.3 58.2 + - - +
73B PRO* 3.0 53.9 - - + +
75B GLN* 5.4 2.2 - - - +
103B ALA* 4.4 14.6 - - - -
104B LEU* 3.8 10.3 + - - +
130C VAL* 5.3 1.1 - - - -
131C VAL* 3.0 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 3.0 39.4 + - - +
25B LEU* 4.5 4.9 - - + +
53B ILE* 3.6 32.1 - - + -
59B ILE* 2.9 20.8 + - + +
60B GLY 3.3 0.9 - - - +
62B MET* 1.3 84.0 - - - +
64B ALA* 1.3 61.4 + - - +
70B LEU* 4.0 12.6 - - + +
71B LEU 3.5 10.1 - - - -
72B VAL* 4.0 13.2 - - + -
104B LEU* 4.2 1.6 - - - -
105B GLY* 3.3 15.6 - - - -
----------------------------------------------------------
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