Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1QWN
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 LEU 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.6 36.8 - - + +
80A LYS* 1.3 71.9 - - - +
82A LYS* 1.3 58.3 + - - +
83A VAL* 3.9 20.4 - - + -
322A TRP* 4.4 5.2 - - + +
323A LYS* 4.0 26.2 - - + -
326A ALA* 4.0 22.4 - - + -
331A THR 5.1 0.4 - - - +
332A ASN* 3.6 19.5 - - - +
333A VAL 5.0 0.2 - - - -
334A LEU* 4.2 17.3 - - + -
371A ASN 2.9 12.3 + - - +
372A VAL* 3.3 15.9 - - + +
373A GLN 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS 3.6 3.0 + - - +
81A LEU* 1.3 71.1 - - - +
83A VAL* 1.3 53.2 + - - +
84A PHE* 3.7 31.8 + - + -
332A ASN* 2.8 15.3 + - - +
333A VAL* 3.3 12.3 - - + +
334A LEU* 2.8 33.1 + - - +
373A GLN* 3.4 21.8 - - + +
375A GLN* 2.7 43.7 + - - +
385A ALA* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.9 20.0 - - + -
82A LYS* 1.3 76.6 - - - +
84A PHE* 1.3 61.0 + - - +
85A VAL* 4.3 6.3 - - + -
322A TRP* 3.8 39.9 - - + -
334A LEU* 3.6 10.5 - - + +
336A ILE* 3.6 28.0 - - + -
372A VAL* 3.9 13.9 - - + -
373A GLN 2.9 8.1 + - - -
374A ALA* 4.0 10.5 - - + -
375A GLN* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.7 33.2 - - + -
83A VAL* 1.3 72.3 - - - +
85A VAL* 1.3 62.3 + - - +
86A VAL* 3.6 15.7 + - + +
333A VAL* 3.7 26.2 - - + -
334A LEU 2.9 12.3 + - - +
335A LEU* 5.0 0.2 - - - -
336A ILE 2.8 27.9 + - - +
375A GLN* 3.5 25.4 - - + -
377A GLY* 4.0 16.6 - - - -
378A THR 5.1 0.2 - - - +
381A GLU* 4.0 35.4 - - + -
382A TYR* 4.0 17.3 - + + -
385A ALA* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 4.3 11.9 - - + +
84A PHE* 1.3 71.7 - - - +
86A VAL* 1.3 61.9 + - - +
87A PRO* 3.3 5.4 - - - +
322A TRP* 4.3 8.5 - - + -
336A ILE* 3.2 21.8 - - + +
338A LEU* 3.8 34.8 - - + -
357A TYR* 4.5 11.7 - - + -
361A PHE* 3.8 29.6 - - + -
375A GLN 2.9 11.9 + - - +
376A PHE* 3.1 16.6 - - + -
377A GLY 2.8 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.8 9.0 - - + +
85A VAL* 1.3 73.0 - - - +
87A PRO* 1.3 65.4 - - - +
88A HIS* 3.5 4.0 + - - -
127A ILE* 3.8 41.1 - - + -
201A TRP* 5.2 4.0 - - + -
335A LEU* 3.6 30.3 - - + -
336A ILE 2.9 12.0 + - - +
337A PRO* 3.6 5.6 - - + +
338A LEU* 2.8 22.1 + - - -
377A GLY 3.5 24.9 - - - +
378A THR 4.0 8.5 - - - +
379A LEU* 4.1 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL 3.3 10.8 - - - +
86A VAL* 1.3 84.1 - - - +
88A HIS* 1.3 61.7 + - - +
124A MET* 3.6 23.8 - - + -
125A LYS* 3.2 28.9 - - + +
126A PHE* 3.5 8.8 - - + +
127A ILE* 3.1 26.7 + - - +
338A LEU* 3.2 15.7 - - + +
344A PHE* 4.0 13.9 - - + -
376A PHE* 4.0 16.2 - - + -
377A GLY 3.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL 3.6 3.6 - - - -
87A PRO* 1.3 76.4 - - - +
89A SER* 1.3 65.4 + - - +
90A HIS 4.3 3.0 + - - -
126A PHE* 3.9 8.3 - - - -
127A ILE* 3.6 25.4 - - + +
201A TRP* 3.6 21.1 + + + +
203A ILE* 3.9 25.3 - - + +
269A TYR* 3.8 14.6 + + + -
337A PRO* 3.8 14.3 - - + +
338A LEU 3.0 17.6 + - - -
339A GLY* 3.2 65.0 + - - -
340A ASP* 3.8 3.7 + - - -
343A ARG* 4.2 0.2 - - - +
344A PHE* 3.4 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 1.3 78.4 - - - +
90A HIS* 1.3 58.8 + - - +
91A ASN* 2.9 32.5 + - - -
110A ILE* 3.8 2.9 - - - +
126A PHE* 3.7 20.8 - - - -
127A ILE 4.5 3.9 + - - +
128A TRP* 4.3 8.1 - - - -
129A ALA 5.9 0.7 + - - -
130A GLU* 4.3 6.1 - - - +
340A ASP 3.6 6.1 - - - -
342A PHE 3.6 1.4 - - - -
343A ARG 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 4.3 2.7 + - - +
89A SER* 1.3 70.1 - - - +
91A ASN* 1.3 60.3 + - - +
92A ASP* 3.1 5.5 + - - -
130A GLU* 4.0 11.0 + - - -
167A MET* 3.8 13.0 - - + +
201A TRP* 6.3 0.2 - - - +
203A ILE* 3.9 26.9 - - + +
204A ASP* 3.4 14.3 + - + -
269A TYR* 3.4 14.8 - - + -
340A ASP 3.0 14.8 + - - +
341A ASP* 3.4 17.5 - - - +
342A PHE* 2.8 27.0 + - - -
471A HIS* 3.5 17.3 - + - -
2003A GUL 3.0 17.5 + - - -
2005A ZN 2.1 29.8 - - - -
----------------------------------------------------------
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