Contacts of the strand formed by residues 118 - 129 (chain A) in PDB entry 3DOY
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 ARG 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.9 13.5 - - - +
45A TYR* 3.2 58.1 - - + -
46A LYS 4.0 3.1 - - - -
47A ASN* 3.9 10.8 - - - +
116A GLY 4.0 1.0 + - - +
117A ASP* 1.3 71.5 - - - +
119A LEU* 1.3 57.3 + - - +
120A GLU* 3.2 46.3 + - - +
140A GLN 3.3 8.5 - - - +
141A VAL* 3.9 14.2 - - + +
142A ASP 4.8 2.5 + - - +
47D ASN* 5.0 1.3 - - - +
118D ARG* 6.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.0 4.1 - - - -
46A LYS 2.8 44.2 + - - +
48A ILE* 4.1 12.8 - - + -
65A PHE* 3.8 29.4 - - + -
70A ILE* 3.9 12.8 - - + -
113A VAL* 4.0 13.9 - - + -
117A ASP 3.8 1.8 - - - -
118A ARG* 1.3 67.7 - - - +
120A GLU* 1.3 59.8 + - - +
121A TYR* 3.7 33.5 + - + +
139A ALA* 3.8 25.4 - - + -
140A GLN 3.8 1.8 - - - +
141A VAL* 4.2 6.0 - - + +
146A VAL* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.8 1.4 + - - -
43A VAL* 4.0 13.9 - - + +
44A ALA 3.4 12.1 - - - +
45A TYR* 3.8 2.9 - - + -
118A ARG* 3.2 35.2 + - - +
119A LEU* 1.3 71.8 - - - +
121A TYR* 1.3 63.3 + - - +
122A HIS* 2.7 33.4 + - + +
138A THR 3.6 0.7 - - - +
139A ALA* 3.2 4.7 - - - -
140A GLN* 2.7 54.1 + - - +
143A GLY 5.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.9 29.2 + - - +
30A VAL* 4.1 5.6 - - + -
42A ILE 3.6 1.4 - - - +
43A VAL* 3.2 6.9 - - - -
44A ALA* 2.5 44.7 + - + +
45A TYR* 4.2 2.5 - - - -
46A LYS* 3.5 26.6 - - + +
65A PHE* 5.0 0.3 - - - -
69A LEU 4.6 2.4 + - - -
70A ILE* 3.7 19.1 - - + -
73A GLY* 3.4 19.8 - - - -
74A MET* 3.6 17.0 - - + -
77A SER* 3.2 27.8 - - - +
119A LEU* 3.7 29.0 - - + +
120A GLU* 1.3 75.5 - - - +
122A HIS* 1.3 62.1 + - - +
123A LEU* 3.8 12.7 - - + +
138A THR 3.8 2.5 - - - -
139A ALA* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 6.0 0.8 + - - -
42A ILE 3.7 4.3 - - - -
43A VAL* 4.0 20.8 - - + +
120A GLU* 2.7 46.8 + - + +
121A TYR* 1.3 77.9 - - - +
123A LEU* 1.3 62.6 + - - +
124A GLU* 4.8 5.6 - - + +
137A GLY* 3.0 6.8 - - - -
138A THR* 2.9 44.0 + - - +
140A GLN* 3.6 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.2 5.7 - - - +
42A ILE* 2.9 47.2 + - + +
74A MET* 3.5 46.9 - - + +
77A SER* 4.0 4.7 - - - -
78A GLY* 4.2 10.8 - - - +
81A LEU* 4.9 1.8 - - + -
121A TYR* 3.8 16.8 - - + -
122A HIS* 1.3 87.6 - - - +
124A GLU* 1.3 63.3 + - - +
135A VAL* 3.9 24.9 - - + -
136A GLY* 3.7 17.0 - - - -
137A GLY 4.0 3.4 - - - +
149A ALA 5.3 0.2 - - - +
151A LEU* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN 3.3 5.8 - - - +
41A LYS* 3.1 22.3 + - - +
122A HIS* 4.8 6.1 - - + +
123A LEU* 1.3 81.2 - - - +
125A VAL* 1.3 63.8 + - - +
126A LEU* 3.3 3.8 + - + +
135A VAL* 3.3 6.4 - - - -
136A GLY 2.9 35.6 + - - +
137A GLY* 5.3 1.3 - - - -
2001A BEN 3.0 59.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN 3.3 36.6 - - - +
40A GLN 2.7 16.9 + - - +
81A LEU* 3.7 20.0 - - + -
124A GLU* 1.3 69.1 - - - +
126A LEU* 1.3 61.2 + - - +
127A LYS* 3.9 11.7 - - - +
128A HIS* 3.9 15.5 - - + -
133A TRP* 3.8 32.5 - - + -
134A GLN 4.0 4.7 - - - +
135A VAL* 4.4 4.3 - - + -
2001A BEN 3.1 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 3.3 4.2 + - + +
125A VAL* 1.3 73.7 - - - +
127A LYS* 1.3 64.8 + - + +
134A GLN* 2.8 17.0 + - + +
135A VAL* 3.6 7.4 - - - +
136A GLY* 3.4 33.7 - - - +
150A GLU* 4.4 20.6 - - + +
2001A BEN 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 3.5 5.8 - - - +
126A LEU* 1.3 83.0 - - + +
128A HIS* 1.3 68.8 + - - +
129A LYS* 2.8 44.9 - - - +
132A ILE* 3.9 4.4 + - - +
133A TRP* 3.6 1.6 - - - -
134A GLN* 2.9 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.6 36.8 + - + +
86A LEU* 5.7 2.9 - - + +
125A VAL* 3.9 15.5 - - + -
127A LYS* 1.3 79.8 - - - +
129A LYS* 1.3 66.6 + - - +
130A GLY 5.1 2.8 + - - -
132A ILE 3.4 4.0 - - - -
133A TRP* 3.5 40.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 2.8 37.9 - - - +
128A HIS* 1.3 79.6 - - - +
130A GLY* 1.3 64.3 + - - +
131A MET 3.3 0.5 + - - -
132A ILE* 2.9 35.3 + - + +
2005A BEN 5.4 0.5 + - - -
----------------------------------------------------------
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