Contacts of the strand formed by residues 111 - 122 (chain B) in PDB entry 4N3E
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 111 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER 3.5 13.2 - - - -
13B PRO* 3.9 3.4 - - - -
14B ILE 3.4 12.3 - - - -
16B PRO* 3.8 6.8 - - - +
107B ALA* 3.5 4.5 - - - -
108B VAL 2.9 32.8 + - - -
109B GLY 3.9 1.0 - - - +
110B GLY* 1.3 77.8 - - - +
112B SER* 1.3 63.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.4 5.9 - - - +
12B SER* 3.0 28.5 + - - +
14B ILE 2.3 29.2 + - - -
15B ALA 3.7 4.3 - - - -
16B PRO* 3.8 18.5 - - - +
19B LEU* 4.0 14.7 - - - +
105B LEU* 5.0 2.2 - - - -
106B GLU 3.2 15.5 - - - -
108B VAL* 4.2 8.0 - - - +
111B GLY* 1.3 73.2 - - - -
113B LYS* 1.3 70.4 + - - +
202B 2AN 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 4.4 16.5 + - - +
10B GLU 3.1 12.1 - - - +
11B GLU* 4.1 23.8 - - + +
105B LEU* 3.5 5.0 - - - +
106B GLU* 2.7 61.6 + - + +
108B VAL* 3.7 16.8 - - + -
112B SER* 1.3 79.5 - - - +
114B GLY* 1.3 64.0 + - - +
202B 2AN 4.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.3 24.9 - - - +
10B GLU 2.8 10.8 + - - +
104B LYS 3.4 9.6 - - - -
105B LEU* 4.0 4.3 - - - -
113B LYS* 1.3 77.4 - - - +
115B LYS* 1.3 66.3 + - - +
116B ILE* 4.0 5.2 - - - -
202B 2AN 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 5.4 8.1 - - - +
7B VAL* 4.0 27.2 - - - +
8B LYS 3.5 3.1 - - - -
9B GLU* 3.8 25.6 - - + +
102B GLU 3.7 3.6 - - - +
103B VAL 4.0 0.2 - - - -
104B LYS* 3.1 35.5 + - + +
114B GLY* 1.3 72.4 - - - +
116B ILE* 1.3 61.1 + - - +
117B THR* 5.0 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.4 2.8 - - - +
8B LYS* 2.8 60.4 + - + +
10B GLU* 5.0 2.2 - - + -
101B TYR* 5.5 2.0 - - + -
102B GLU 3.4 11.0 - - - +
103B VAL* 4.2 15.3 - - + -
104B LYS 5.2 0.2 - - - +
105B LEU* 5.4 0.2 - - + -
114B GLY* 4.2 4.3 - - - -
115B LYS* 1.3 84.2 - - - +
117B THR* 1.3 74.2 + - - +
118B VAL* 4.2 4.3 - - + -
202B 2AN 3.4 77.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 4.2 7.9 - - - +
6B ILE 3.2 11.4 - - - -
7B VAL* 3.2 29.2 - - + -
100B VAL 3.8 2.3 + - - +
101B TYR* 3.9 0.9 - - - -
102B GLU* 3.3 43.3 + - + +
115B LYS* 5.0 10.8 - - - +
116B ILE* 1.3 77.9 - - - +
118B VAL* 1.3 67.3 + - - +
119B THR* 5.1 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 3.0 19.6 - - - +
6B ILE* 3.0 31.4 + - + +
8B LYS* 3.7 21.8 - - - +
99B VAL* 3.8 19.1 - - + -
100B VAL 3.7 2.5 - - - +
101B TYR* 3.5 39.5 - - + -
116B ILE* 4.2 5.4 - - + -
117B THR* 1.3 78.3 - - - +
119B THR* 1.3 62.6 + - - +
120B TYR* 4.0 17.5 + - + +
202B 2AN 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 3.5 5.5 - - - +
5B THR* 3.6 19.1 - - + -
99B VAL* 3.5 2.9 - - - -
100B VAL* 2.9 60.3 + - + +
102B GLU* 6.1 2.2 - - + -
117B THR* 5.4 3.6 - - - +
118B VAL* 1.3 72.1 - - - +
120B TYR* 1.3 60.7 + - - +
121B HIS* 2.4 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 3.2 20.6 - - - +
4B TYR* 3.4 21.5 + - + +
5B THR 4.8 0.6 - - - +
6B ILE* 5.6 6.3 - - + -
96B ILE* 4.6 12.3 - - + -
98B LYS 4.3 2.0 - - - -
99B VAL* 3.5 31.6 - - + -
101B TYR* 4.6 4.0 + - - -
118B VAL* 4.0 25.6 + - + +
119B THR* 1.3 74.3 + - - +
121B HIS* 1.3 60.2 + - - +
122B PRO* 3.3 7.6 - - - +
128B VAL* 4.8 6.7 - - + +
129B ASN 6.1 0.7 - - - -
132B GLU* 3.2 55.6 + - + -
133B VAL* 4.7 20.0 - - + -
136B GLY* 3.6 18.7 - - - -
137B GLU 6.0 0.7 - - - -
201B 2AN 4.0 11.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.8 9.6 - - + -
3B ALA* 3.4 16.6 - - + +
96B ILE* 3.7 5.8 - - - +
97B GLU* 3.0 39.7 + - - +
98B LYS* 2.9 32.2 + - + +
100B VAL* 4.0 20.9 - - + +
119B THR* 2.4 43.4 + - - +
120B TYR* 1.3 70.7 - - - +
122B PRO* 1.4 66.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 5.8 0.2 - - - +
2B ALA 4.1 15.7 - - - +
3B ALA* 4.1 9.6 - - + +
95B ASN 3.3 12.8 - - - +
96B ILE* 4.6 2.9 - - + -
97B GLU* 3.0 18.2 - - - +
120B TYR 3.3 11.9 - - - +
121B HIS* 1.4 86.2 - - + +
123B LYS* 1.3 66.0 + - - +
126B CYS 3.1 22.4 - - - +
127B THR* 4.6 0.9 - - - +
128B VAL* 3.9 22.9 - - + -
----------------------------------------------------------
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