Contacts of the strand formed by residues 89 - 95 (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 GLY 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 6.0 1.1 - - - -
87A ALA 3.7 1.2 - - - -
88A ASP* 1.3 81.3 - - - +
90A LEU* 1.3 66.6 + - - -
108A LEU* 4.0 5.2 - - - -
129A PHE 3.5 6.5 - - - -
131A THR* 4.5 5.4 - - - -
218A ALA* 3.0 28.2 - - - +
219A SER 3.6 3.5 + - - +
226A LEU* 3.9 14.4 - - - +
228A VAL* 3.9 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.8 0.7 - - + -
75A PHE* 3.8 25.1 - - + -
77A PHE* 4.1 24.0 - - + -
79A LEU* 4.4 4.7 - - + -
89A GLY* 1.3 80.0 - - - +
91A ALA* 1.3 63.7 + - - +
108A LEU* 4.2 5.7 - - - +
128A GLU* 3.7 0.7 - - - +
129A PHE* 2.7 67.3 + - + +
160A TRP* 5.1 1.3 - - + -
216A ILE* 4.3 12.8 - - + -
217A SER 3.0 14.8 - - - +
218A ALA* 4.2 3.1 - - + +
228A VAL* 3.7 28.0 - - + -
230A ILE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 1.3 82.7 - - - +
92A PHE* 1.3 63.3 + - - +
93A PHE* 4.1 1.4 - - - -
108A LEU* 4.1 4.7 - - + -
110A LEU* 4.0 26.9 - - + -
126A ALA* 4.6 0.2 - - + -
127A VAL 3.0 16.6 - - - +
128A GLU* 3.8 12.3 - - + -
129A PHE* 4.3 0.4 - - - -
216A ILE* 3.1 9.8 - - - +
217A SER* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.2 11.0 - + - -
73A THR* 3.8 25.4 - - + -
75A PHE* 3.8 12.5 - + + -
91A ALA* 1.3 72.7 - - - +
93A PHE* 1.3 62.9 + - - +
94A LEU* 3.7 22.9 - - + -
126A ALA* 3.1 4.2 - - - +
127A VAL* 2.8 35.1 + - + +
129A PHE* 4.7 1.4 - - - -
175A ILE* 3.5 38.1 - - + -
214A VAL* 3.9 22.7 - - + -
215A GLY 3.3 14.8 - - - -
216A ILE* 4.2 5.2 - - + +
233A TRP* 3.7 34.1 - + - -
235A PHE* 4.1 13.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.8 31.9 - - + -
53A LEU* 3.2 30.7 - - + -
91A ALA 4.1 6.5 - - - -
92A PHE* 1.3 80.8 - - - +
94A LEU* 1.3 80.1 + - - +
95A ALA* 4.0 14.1 - - + -
110A LEU* 3.4 21.5 - - + -
124A VAL* 3.9 9.2 - - + -
125A VAL 3.2 6.7 - - - +
126A ALA* 3.3 19.3 - - + +
213A ARG 5.1 0.4 - - - -
214A VAL* 3.5 5.0 - - - +
215A GLY* 3.0 54.9 + - - -
216A ILE 3.4 14.8 - - - -
217A SER* 4.1 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 6.2 1.1 - - + -
60A LEU* 3.9 26.0 - - + -
71A PHE* 4.1 29.2 - - + -
92A PHE* 3.7 22.4 - - + -
93A PHE* 1.3 81.4 - - - +
95A ALA* 1.3 64.0 + - - +
124A VAL* 3.4 6.4 - - - +
125A VAL* 2.8 36.8 + - + +
204A MET* 4.5 9.4 - - + -
208A LEU* 3.7 18.0 - - + +
212A VAL* 4.0 13.7 - - + -
213A ARG 3.4 6.1 - - - +
214A VAL* 4.1 16.4 - - + -
235A PHE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 5.6 0.2 - - - +
53A LEU* 6.1 0.4 - - + -
93A PHE* 4.0 18.6 - - + -
94A LEU* 1.3 77.5 - - - +
96A PRO* 1.3 75.2 - - + +
99A SER* 3.7 21.3 - - - +
123A GLN 3.5 9.0 - - - +
124A VAL* 4.7 2.7 - - + -
208A LEU* 4.9 2.2 - - - -
209A PRO* 5.2 0.2 - - - -
212A VAL* 3.1 9.9 - - - +
213A ARG* 2.8 32.5 + - + +
----------------------------------------------------------
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