Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 3LZN
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 4.6 1.6 - - - -
76A ASP* 3.3 11.7 - - - -
111A GLY 3.3 2.4 + - - -
112A VAL* 1.3 76.0 - - - +
114A ASN* 1.3 64.2 + - - -
115A TYR* 3.4 10.2 - - - -
153A LYS* 3.5 14.5 - - - +
154A TYR 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.4 7.6 - - - +
75A THR* 2.8 39.2 + - - +
76A ASP* 2.9 29.3 + - - +
113A GLY* 1.3 73.4 - - - -
115A TYR* 1.3 59.9 + - - +
152A PHE 3.7 4.7 - - - +
153A LYS* 3.8 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.8 19.7 - - + -
73A LYS 3.1 20.2 - - - -
74A ASN* 3.0 31.4 + - + -
75A THR* 4.4 1.1 - - - +
102A MET* 3.6 17.0 - - + -
110A PHE* 2.9 30.3 + + - -
111A GLY 2.6 29.1 + - - -
113A GLY 3.4 13.7 - - - -
114A ASN* 1.3 77.6 - - - +
116A GLU* 1.3 64.7 + - - +
151A LYS* 3.4 6.4 - - - +
152A PHE* 2.8 56.5 + + + +
154A TYR* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU 3.7 0.9 - - - +
72A LEU* 3.5 4.8 - - - +
73A LYS* 2.8 62.0 + - + +
75A THR* 3.4 25.8 - - + +
115A TYR* 1.3 74.9 - - - +
117A LEU* 1.3 62.7 + - - +
118A THR* 5.2 3.4 - - - +
149A ASP* 6.5 0.4 - - + -
150A TYR 3.3 6.7 - - - +
151A LYS* 3.5 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 21.8 - - + -
19A ALA* 3.9 7.6 - - + -
43A LEU* 3.9 31.4 - - + -
70A TYR* 4.1 9.6 - - + -
71A GLU 3.4 14.8 - - - +
72A LEU* 4.0 17.7 - - + -
115A TYR 4.2 0.4 - - - -
116A GLU* 1.3 74.8 - - - +
118A THR* 1.3 71.7 + - - +
119A PHE* 3.8 27.4 - - + -
149A ASP* 3.3 3.1 - - - +
150A TYR* 2.7 47.6 + - + +
152A PHE* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.1 8.1 - - - +
71A GLU* 2.8 40.7 + - - +
116A GLU* 5.2 3.5 - - - +
117A LEU* 1.3 75.1 - - - +
119A PHE* 1.3 72.2 + - - +
120A TYR* 3.5 35.9 + - + +
147A LYS* 3.8 12.6 - - + -
148A VAL 3.3 6.5 - - - +
149A ASP* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.1 11.2 - - + -
18A ALA 4.3 2.0 - - - -
19A ALA* 3.8 15.0 - - + -
43A LEU* 4.3 5.6 - - + -
44A GLU 4.2 3.4 - - - -
45A ALA* 3.5 30.1 - - + -
68A ILE* 4.2 3.8 - - + -
69A ALA 3.3 4.7 - - - +
70A TYR* 3.9 11.7 - - + -
85A LEU* 3.6 21.1 - - + -
117A LEU* 3.8 29.6 - - + +
118A THR* 1.3 78.8 - - - +
120A TYR* 1.3 61.3 + - - +
121A ILE* 4.1 14.7 - - + +
146A PHE 3.8 0.2 - - - +
147A LYS* 3.0 8.0 - - - +
148A VAL* 2.9 40.0 + - + +
150A TYR* 3.7 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 3.5 1.0 - - - +
68A ILE* 3.3 4.3 - - - -
69A ALA* 2.8 54.6 + - + +
70A TYR 4.5 1.3 - - - -
71A GLU* 2.5 41.2 + - + -
82A ARG* 6.1 1.8 - - + -
118A THR* 3.5 22.4 + - + +
119A PHE* 1.3 71.4 - - - +
121A ILE* 1.3 62.1 + - - +
122A SER* 5.6 0.2 - - - -
146A PHE 3.4 5.4 - - - +
147A LYS* 3.8 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 5.2 0.9 - - + -
17A ILE* 4.0 17.0 - - + -
47A ILE* 4.1 17.0 - - + -
66A LEU* 4.3 17.7 - - + -
67A THR 3.3 5.8 - - - +
68A ILE* 4.0 16.2 - - + -
119A PHE* 4.1 19.5 - - + +
120A TYR* 1.3 80.6 - - - +
122A SER* 1.3 71.6 + - - +
143A PHE* 3.9 9.4 - - + -
145A PRO* 3.3 4.8 - - - +
146A PHE* 2.8 76.8 + - + +
148A VAL* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.6 10.0 - - - +
67A THR* 2.9 34.1 + - - +
120A TYR 5.6 0.3 - - - -
121A ILE* 1.3 74.2 - - - +
123A ASN* 1.3 66.3 + - - +
126A LYS* 4.0 29.4 - - - +
143A PHE* 3.7 5.6 - - - -
145A PRO* 3.6 26.6 - - - +
----------------------------------------------------------
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