Contacts of the strand formed by residues 120 - 126 (chain B) in PDB entry 3L43
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 ILE 120 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 3.6 39.3 - - + +
68B PRO 2.9 10.7 + - - +
69B LEU* 3.5 23.8 - - + +
70B VAL 2.7 31.4 + - - +
83B PHE* 3.8 28.7 - - + -
85B HIS* 4.9 2.7 - - - +
101B ILE* 4.1 19.3 - - + +
104B GLU* 4.2 15.5 - - + -
105B THR* 3.6 30.1 - - + -
119B PRO* 1.4 70.4 - - - +
121B ASN* 1.3 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.4 28.6 - - - +
82B GLU 4.2 0.2 - - - +
83B PHE* 3.6 7.8 - - - -
84B LEU* 3.1 66.6 + - + +
85B HIS* 5.3 1.2 + - - -
119B PRO* 3.9 24.2 + - - +
120B ILE* 1.3 73.9 - - - +
122B LEU* 1.3 59.6 + - - +
123B ARG* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 4.0 22.2 - - + -
69B LEU* 4.1 17.0 - - + -
70B VAL 2.9 11.5 + - - +
71B LEU* 3.4 11.2 - - + +
72B GLN* 2.9 26.9 + - - +
81B ALA* 4.0 14.4 - - + -
82B GLU 3.8 9.0 - - - +
83B PHE* 3.7 31.4 - - + -
97B VAL* 3.8 21.8 - - + -
101B ILE* 4.0 13.0 - - + -
120B ILE 3.7 0.6 + - - -
121B ASN* 1.3 73.5 - - - +
123B ARG* 1.3 73.4 + - - +
124B VAL* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 3.0 42.0 + - + +
74B ILE* 3.8 15.9 - - + +
81B ALA* 3.2 6.6 - - - +
82B GLU* 2.8 47.7 + - + +
84B LEU* 5.5 13.9 - - + +
121B ASN 5.9 0.9 - - - -
122B LEU* 1.3 73.3 - - - +
124B VAL* 1.3 60.4 + - - +
125B TYR* 2.9 41.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.0 27.8 - - + -
56B PHE* 5.1 2.0 - - + -
71B LEU* 3.8 18.6 - - + -
72B GLN 2.9 10.3 + - - -
73B LEU* 3.5 16.2 - - + -
74B ILE* 2.8 31.3 + - - +
80B TYR 3.9 1.6 - - - -
81B ALA* 3.9 15.3 - - + -
94B PHE* 4.0 22.7 - - + -
122B LEU* 4.1 10.9 + - + -
123B ARG* 1.3 76.6 - - - +
125B TYR* 1.4 62.4 + - - +
126B SER* 3.8 9.4 + - - -
129B VAL* 3.9 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.2 40.8 - - + -
76B SER* 3.8 15.0 - - - -
78B ALA 3.2 16.2 - - - +
79B GLU* 3.3 2.6 - - - +
80B TYR* 2.9 82.7 + + + +
82B GLU* 4.4 4.7 - - + +
123B ARG* 2.9 52.1 + - + -
124B VAL* 1.4 72.0 - - - +
126B SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.2 4.6 + - - -
74B ILE 2.9 11.4 + - - +
75B THR* 3.4 6.4 - - - -
76B SER 3.1 18.2 + - - -
79B GLU* 4.0 11.0 + - - +
94B PHE* 6.1 0.2 - - - -
124B VAL* 3.8 8.8 + - - -
125B TYR* 1.3 74.7 - - - +
127B PRO* 1.4 69.5 - - - +
128B HIS* 3.1 31.3 + - - +
129B VAL* 3.5 26.8 + - - +
----------------------------------------------------------
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