Contacts of the strand formed by residues 117 - 123 (chain A) in PDB entry 1QN9
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 ASN 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN 4.7 0.2 - - - -
28A ILE* 3.4 3.8 - - - +
29A VAL* 2.8 40.6 + - + +
115A ILE* 3.7 1.4 - - - +
116A GLN* 1.3 81.6 - - - +
118A ILE* 1.3 67.3 + - - +
119A VAL* 3.8 9.7 - - - +
173A THR* 3.5 3.8 + - - -
174A GLY* 2.8 36.2 + - - -
175A ALA 3.2 6.7 + - - -
206C A 3.5 28.8 + - - -
207C A 3.5 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.5 31.6 - - + -
27A ASN 3.6 3.8 - - - -
28A ILE* 3.7 22.0 - - + -
87A GLU* 3.8 15.3 - - + +
115A ILE* 3.8 13.5 - - + -
117A ASN* 1.3 88.3 + - - +
119A VAL* 1.3 65.7 + - - +
120A GLY 4.2 0.2 - - - -
172A ILE 3.9 1.4 - - - +
173A THR* 3.8 2.6 - - - -
174A GLY 3.7 11.3 + - - -
175A ALA* 2.8 19.4 + - + +
176A LYS 3.8 4.0 - - - +
177A MET* 3.6 41.3 - - - +
178A ARG* 3.6 4.7 - - - +
181A THR* 4.1 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 3.8 - - - -
26A GLN* 2.8 33.5 + - + -
27A ASN* 2.9 26.6 + - + +
117A ASN* 3.8 7.4 - - - +
118A ILE* 1.3 79.9 - - - +
120A GLY* 1.3 63.0 + - - +
171A VAL* 4.2 5.4 - - + -
172A ILE 3.5 7.4 - - - +
173A THR* 3.4 18.4 - - - +
206C A 3.8 8.1 - - + -
223D T 3.5 20.2 - - - +
224D G 3.7 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.9 0.9 - - - -
24A THR 3.2 14.4 - - - -
25A LEU* 4.3 2.2 - - - -
26A GLN* 4.3 2.9 - - - -
118A ILE 4.2 0.4 - - - -
119A VAL* 1.3 74.8 - - - +
121A SER* 1.3 63.1 + - - -
171A VAL* 3.4 5.9 - - - +
172A ILE* 2.8 38.0 + - - +
181A THR* 4.4 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.2 1.3 - - - +
24A THR* 2.8 35.6 + - - +
26A GLN* 3.0 31.5 + - - +
120A GLY* 1.3 74.9 - - - -
122A CYS* 1.3 64.9 + - - +
170A ILE 3.1 14.4 - - - -
171A VAL* 4.1 13.5 - - - -
172A ILE* 4.2 2.8 - - - +
224D G 3.9 14.5 + - - -
225D T 5.4 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.9 15.7 - - + -
22A VAL 4.7 1.8 - - - +
23A PRO* 3.9 16.2 - - + -
121A SER* 1.3 77.0 - - - +
123A ASP* 1.3 60.7 - - - +
124A VAL 4.2 0.4 - - - -
168A GLY 3.9 0.2 - - - +
169A LYS* 3.6 5.4 - - - +
170A ILE* 2.9 31.9 + - - +
172A ILE* 4.1 12.1 - - - -
185A PHE* 3.2 44.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.1 12.7 - - - +
122A CYS* 1.3 77.7 - - - +
124A VAL* 1.3 63.3 + - - +
125A LYS* 3.0 61.3 + - - +
167A SER 4.4 3.6 - - - +
168A GLY 3.5 10.4 - - - +
169A LYS* 3.1 33.4 + - - +
----------------------------------------------------------
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