Contacts of the helix formed by residues 67 - 78 (chain B) in PDB entry 4L5L
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 GLN 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER 4.7 0.2 - - - +
94A MET* 3.3 25.6 - - + +
97A GLY* 3.2 27.8 + - - -
98A GLY* 3.3 11.9 + - - +
101A ASP* 3.0 17.2 - - - +
52B LEU* 6.5 0.2 - - + -
54B ASN* 3.8 12.3 + - - +
56B PRO 3.8 5.1 + - - -
66B THR* 1.3 84.5 + - - +
68B SER* 1.3 66.2 + - - +
69B LEU* 3.2 3.8 - - + +
70B ALA* 3.0 13.7 + - + +
71B ILE* 2.9 23.4 + - - +
301B GSH 3.0 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.9 35.4 - - - +
17B ILE* 3.8 8.9 - - - +
56B PRO* 3.9 18.3 - - - +
67B GLN* 1.3 68.9 - - - +
69B LEU* 1.3 59.7 + - - +
71B ILE* 3.4 3.0 + - - +
72B LEU* 2.9 29.9 + - - +
100B VAL* 6.0 2.1 - - - +
301B GSH 2.6 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.9 17.5 - - + -
93A SER* 6.4 0.2 - - - -
67B GLN* 3.2 4.0 - - + +
68B SER* 1.3 81.5 + - - +
70B ALA* 1.3 61.3 + - - +
72B LEU* 4.3 7.2 - - + -
73B ARG* 2.9 41.0 + - + +
93B SER 5.9 0.2 - - - +
96B GLU* 3.9 45.5 - - + +
97B GLY* 5.4 2.5 - - - +
100B VAL* 4.6 15.7 - - + -
150B HIS* 5.1 0.4 - - + -
154B MET* 4.0 21.8 - - + -
301B GSH 4.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 3.9 9.0 - - - +
93A SER* 3.6 20.0 + - - +
94A MET* 3.3 31.9 - - + +
65B LEU* 3.8 6.4 - - + +
66B THR 3.6 11.7 - - - +
67B GLN* 3.0 12.3 + - + +
69B LEU* 1.3 79.4 - - - +
71B ILE* 1.3 57.5 + - - +
73B ARG* 3.8 1.8 - - - +
74B TYR* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.7 2.2 - - + -
17B ILE* 3.9 25.6 - - + -
56B PRO* 3.7 37.9 - - + +
57B TYR* 3.7 21.8 - - - -
58B TYR* 3.7 33.2 - - + +
65B LEU* 4.0 22.4 - - + +
66B THR 4.2 1.1 - - - +
67B GLN 2.9 18.3 + - - +
68B SER 3.8 5.2 - - - +
70B ALA* 1.3 73.7 - - - +
72B LEU* 1.3 65.6 - - - +
74B TYR* 3.3 3.4 + - + +
75B ILE* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 3.5 34.3 - - + +
17B ILE* 3.9 17.7 - - + +
20B LEU* 3.7 25.9 - - + +
68B SER 2.9 15.5 + - - +
69B LEU* 3.6 9.6 - - + +
70B ALA 3.4 0.2 - - - -
71B ILE* 1.3 76.2 - - - +
73B ARG* 1.3 58.3 + - - +
75B ILE* 3.4 4.8 + - - +
76B ALA* 2.9 28.6 + - - +
150B HIS* 3.8 19.7 - - + -
154B MET* 3.3 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.3 25.9 - - - +
89A ARG* 6.2 2.0 - - - +
90A ALA* 6.3 0.9 - - - -
93A SER* 3.7 21.6 + - - +
69B LEU* 2.9 32.6 + - + +
70B ALA* 3.9 4.5 - - - +
71B ILE 3.2 0.2 - - - -
72B LEU* 1.3 75.2 - - - +
74B TYR* 1.3 56.6 + - - +
76B ALA* 4.1 5.8 - - - -
77B ASP* 2.6 36.9 + - - +
82B ILE* 3.9 36.1 + - + +
89B ARG* 4.9 6.3 + - - +
92B ILE* 4.3 6.5 - - - +
93B SER* 3.5 16.1 + - - +
96B GLU* 2.7 56.7 + - - +
150B HIS* 4.4 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.8 28.0 - - + -
87A VAL* 4.3 9.2 - - + +
90A ALA* 3.8 13.1 - - + +
58B TYR* 3.8 33.4 - + - -
60B ASP* 5.3 4.4 + - - -
63B PHE* 3.6 29.7 - + - -
65B LEU* 3.7 13.7 - - + -
70B ALA 2.9 17.2 + - - +
71B ILE 3.3 4.7 + - - +
73B ARG* 1.3 75.9 - - - +
75B ILE* 1.3 70.3 + - + +
77B ASP* 3.6 4.8 - - - +
78B LYS* 3.0 65.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.8 19.3 - - + -
20B LEU* 3.4 32.1 - - + -
21B LEU* 3.5 41.5 - - + -
24B VAL* 4.7 2.9 - - + -
26B ASP* 6.1 0.2 - - - -
58B TYR* 4.4 12.6 - - + +
71B ILE* 3.1 22.1 + - + +
72B LEU 3.8 1.8 - - - +
74B TYR* 1.3 88.1 - - + +
76B ALA* 1.3 62.1 + - - +
78B LYS* 3.5 4.2 + - - +
79B HIS* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.2 1.8 - - - +
72B LEU 2.9 18.3 + - - +
73B ARG* 3.8 4.3 - - - +
75B ILE* 1.3 75.2 - - - +
77B ASP* 1.3 64.7 + - - +
79B HIS 2.9 9.7 + - - -
81B MET* 2.9 41.7 + - + +
82B ILE* 3.9 8.5 - - + -
150B HIS* 3.6 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.5 20.7 - - + +
89A ARG* 2.9 48.6 + - - +
73B ARG* 2.6 22.9 + - + +
74B TYR* 3.6 6.3 - - - +
76B ALA* 1.3 71.0 - - - +
78B LYS* 1.3 54.6 + - - +
79B HIS 2.7 12.1 + - - -
80B ASN* 2.8 15.6 + - - +
82B ILE* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.7 34.2 - - + +
74B TYR* 3.0 55.7 + - + +
75B ILE* 3.8 7.4 - - - +
76B ALA 3.4 0.2 - - - -
77B ASP* 1.3 71.0 - - - +
79B HIS* 1.3 70.9 + - + +
80B ASN* 3.6 1.9 + - - +
----------------------------------------------------------
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