Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 1GNZ
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 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.5 11.1 - - - +
58A VAL 3.3 6.3 + - - -
59A GLN* 3.4 20.6 + - - +
97A PRO* 3.2 30.2 - - - +
209A PRO* 3.3 17.1 - - - +
210A GLU* 1.3 76.9 - - - +
212A VAL* 1.3 63.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 3.1 8.3 - - - +
58A VAL* 2.7 58.2 + - + +
60A LEU* 3.8 27.1 - - + -
94A LEU* 4.0 22.9 - - + -
95A ALA 3.1 20.0 - - - +
97A PRO* 4.3 2.7 - - - -
208A LEU* 4.1 16.2 - - + -
209A PRO* 3.9 10.3 - - + +
211A SER* 1.3 80.6 - - - +
213A ARG* 1.3 68.2 + - - +
214A VAL* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 5.0 9.9 - - - +
53A LEU* 4.3 29.2 - - + +
54A TYR 3.4 17.8 + - - +
55A SER* 2.8 37.0 + - - +
56A ASP 5.1 1.1 - - - -
57A PRO* 3.6 17.9 - - - +
93A PHE* 3.9 0.5 - - - +
94A LEU* 3.4 4.7 - - - -
95A ALA* 2.8 31.9 + - + +
96A PRO 4.2 2.9 - - - +
97A PRO* 2.4 58.6 + - + +
212A VAL* 1.3 79.0 - - - +
214A VAL* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.9 34.5 - - + -
53A LEU* 3.5 4.0 - - - -
54A TYR* 2.9 31.3 + - + +
56A ASP 5.5 0.2 + - - -
58A VAL* 4.2 15.1 - - + +
92A PHE* 3.9 13.5 - - + -
93A PHE 3.5 4.0 - - - -
94A LEU* 4.1 22.2 - - + -
212A VAL* 4.8 1.6 - - + -
213A ARG* 1.3 77.7 - - - +
215A GLY* 1.3 58.0 + - - +
233A TRP* 3.5 5.1 - - + -
235A PHE* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 3.1 13.9 - - - -
53A LEU* 3.8 11.5 - - - +
92A PHE* 3.3 11.4 - - - -
93A PHE* 3.0 37.5 + - - -
213A ARG 4.1 0.2 + - - -
214A VAL* 1.3 76.7 - - - +
216A ILE* 1.3 63.3 + - - -
233A TRP* 3.5 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.1 6.3 - - + -
35A LEU* 3.8 21.3 - - + +
51A ARG* 3.2 2.9 - - - +
52A ALA 2.8 31.7 + - - +
75A PHE* 3.9 20.0 - - + -
90A LEU* 4.3 13.5 - - + -
91A ALA 3.1 15.5 - - - +
92A PHE* 4.2 7.6 - - + -
93A PHE* 3.4 2.2 - - - -
215A GLY* 1.3 80.4 - - - +
217A SER* 1.3 64.8 + - - +
230A ILE* 4.1 24.0 - - + -
233A TRP* 3.7 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.6 5.6 - - - -
50A GLY 3.1 4.7 - - - -
51A ARG* 3.2 34.3 - - - -
90A LEU* 3.0 7.1 - - - +
91A ALA* 2.9 32.8 + - - +
93A PHE* 4.1 2.7 - - - -
108A LEU* 2.7 25.8 + - - +
110A LEU* 3.6 15.4 - - - +
216A ILE* 1.3 74.0 - - - +
218A ALA* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.4 27.5 - - + +
36A CYS* 3.7 8.5 - - - -
49A ALA* 3.4 1.6 - - - +
50A GLY 2.9 28.1 + - - +
89A GLY 3.0 21.5 - - - +
90A LEU* 4.2 3.6 - - + +
108A LEU* 4.5 7.3 - - - +
217A SER* 1.3 75.3 - - - +
219A SER* 1.3 63.8 + - - +
228A VAL* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 3.7 2.2 - - - -
48A SER 2.9 13.9 - - - -
49A ALA* 4.3 1.1 - - - -
88A ASP* 3.0 27.5 + - - +
89A GLY 3.6 5.5 + - - +
104A ALA* 3.9 12.6 - - - -
105A GLY 2.5 29.4 + - - -
108A LEU* 3.3 21.2 - - - +
109A GLY 4.2 0.7 - - - -
218A ALA* 1.3 80.1 - - - +
220A THR* 1.3 66.8 + - - +
226A LEU* 5.6 0.3 - - - +
228A VAL* 6.1 0.2 - - - +
----------------------------------------------------------
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