Contacts of the strand formed by residues 102 - 110 (chain A) in PDB entry 4WGK
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 TYR 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER 6.1 0.4 - - - -
101A GLY* 1.3 79.4 - - - -
103A HIS* 1.3 64.9 + - - +
104A ILE* 4.0 14.3 + - + -
144A MET* 5.0 2.5 - - + -
145A ALA 3.5 14.1 - - - +
146A GLU* 4.6 8.3 - - - -
147A PRO* 5.4 0.2 - - + -
240A PRO* 3.7 2.3 - - - +
241A GLY 3.0 33.8 + - - +
242A LYS* 5.2 1.1 - - - -
243A ILE* 3.6 33.9 - - + -
419A VAL* 3.2 25.7 - - + -
420A THR* 3.1 9.2 + - + -
421A GLY 2.7 44.5 + - - -
423A LEU* 3.5 30.3 - - + -
529A LEU* 4.1 1.5 - - + -
530A GLY* 3.8 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 1.3 73.3 - - - +
104A ILE* 1.3 60.5 + - - +
144A MET* 3.4 3.6 - - - -
145A ALA* 2.9 37.4 + - + +
146A GLU 3.5 12.1 + - - -
147A PRO* 2.9 35.2 + - + +
148A ASP 5.0 0.4 - - - -
149A GLY* 4.4 7.2 - - - -
238A MET* 3.3 25.2 - - + +
239A LYS* 3.4 4.6 + - - +
240A PRO* 3.5 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 4.1 14.4 - - + +
103A HIS* 1.3 79.2 - - - +
105A GLY* 1.3 68.6 + - - +
106A VAL* 4.4 2.9 - - + -
143A ILE 3.4 5.4 - - - +
144A MET* 4.7 5.6 - - + -
237A ASN 3.9 1.9 - - - +
238A MET* 3.2 2.5 - - - -
239A LYS* 2.8 41.0 + - - +
241A GLY* 4.0 3.4 - - - +
242A LYS 3.5 36.6 - - - +
243A ILE* 3.6 21.8 - - + -
286A MET* 4.0 33.9 - - + -
287A VAL 4.3 5.8 - - - +
294A LEU* 4.2 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 1.3 75.5 - - - +
106A VAL* 1.3 67.4 + - - +
142A PHE* 3.5 0.7 - - - -
143A ILE* 2.8 35.8 + - - -
234A ALA* 3.4 27.3 - - - +
237A ASN 4.0 3.1 - - - -
238A MET* 3.9 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 4.4 13.2 - - + -
105A GLY* 1.3 79.7 - - - +
107A GLY* 1.3 59.2 + - - +
141A ALA 3.4 6.7 - - - +
142A PHE* 3.5 25.6 - - + -
233A ILE* 3.8 7.6 - - - +
234A ALA* 3.4 16.3 + - - +
237A ASN* 4.7 6.9 + - - +
286A MET* 4.4 4.9 - - - -
294A LEU* 3.5 35.0 - - + +
295A GLY* 4.6 2.9 - - - -
340A PRO 4.3 5.8 - - - +
342A VAL* 4.0 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 1.3 76.5 - - - +
108A ARG* 1.3 60.1 + - - +
139A SER 3.8 0.3 - - - +
140A ARG* 3.3 4.5 - - - -
141A ALA 2.9 33.4 + - - +
230A SER* 3.6 19.7 - - - -
233A ILE* 3.8 13.0 - - - -
234A ALA* 3.8 0.8 - - - +
342A VAL* 3.9 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 1.3 75.1 - - - +
109A ALA* 1.3 65.7 + - - +
138A TYR* 3.7 29.8 - - + -
139A SER 3.3 3.8 - - - -
140A ARG* 3.4 34.8 - - + +
229A LYS* 5.4 0.5 - - - -
230A SER* 4.3 0.7 - - - -
233A ILE* 3.6 15.3 - - - +
327A GLU* 2.9 25.7 + - - -
331A ASN* 4.5 0.8 - - - +
337A GLY* 3.0 35.5 + - - +
338A GLN* 3.1 16.0 - - - +
339A GLY 2.9 23.4 + - - +
341A PHE 3.1 19.4 + - - -
342A VAL* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 1.3 77.0 - - - +
110A ASP* 1.3 63.1 + - - +
138A TYR* 3.2 7.9 - - - -
139A SER* 2.7 38.1 + - - -
226A GLY 3.3 23.6 - - - +
229A LYS* 3.6 25.6 - - + +
230A SER* 3.5 15.5 - - - +
233A ILE* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 1.3 70.5 - - - +
111A CYS* 1.3 58.7 + - - +
112A THR* 2.7 34.8 + - - -
136A ARG* 3.0 35.6 + - - +
137A LEU 3.1 7.0 - - - +
138A TYR* 3.9 13.5 - - + -
222A HIS* 3.6 21.9 + - + +
226A GLY* 3.4 16.1 - - - -
229A LYS* 5.2 8.9 - - - +
690A HIS 4.8 3.8 - - - +
691A GLN* 4.8 5.7 - - + +
----------------------------------------------------------
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