Contacts of the helix formed by residues 93 - 103 (chain B) in PDB entry 2YVE
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 SER 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 6.1 0.2 - - - +
91B ASN 3.4 3.5 + - - -
92B VAL* 1.3 80.0 - - - +
94B ARG* 1.3 65.9 + - - +
95B PRO* 3.5 10.1 - - - +
96B GLU* 3.3 26.5 + - - +
97B LEU* 3.0 20.4 + - - +
151B TYR* 3.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.8 29.7 + - + +
102A ASP* 5.1 9.7 + - - +
18B GLY* 2.9 30.6 + - - +
19B GLU* 5.6 1.3 - - - -
20B TYR 5.0 7.5 + - - -
93B SER* 1.3 70.7 - - - +
95B PRO* 1.3 73.7 - - + +
97B LEU* 3.2 4.0 + - - +
98B LEU* 3.0 51.9 + - + +
151B TYR* 3.3 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.3 44.6 - - + +
15B ASP* 4.8 7.0 - - - +
17B ILE* 3.7 13.1 - - + +
18B GLY* 4.0 13.5 - - - -
93B SER* 3.5 14.1 - - - +
94B ARG* 1.3 95.9 - - + +
96B GLU* 1.3 60.8 + - - +
98B LEU* 3.8 1.5 - - + -
99B LEU* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.5 45.0 - - + +
92B VAL* 3.9 7.2 - - + +
93B SER* 3.3 23.3 + - - +
94B ARG 3.2 0.4 - - - -
95B PRO* 1.3 79.2 - - - +
97B LEU* 1.3 58.5 + - - +
99B LEU* 3.3 2.3 + - - +
100B LEU* 2.9 43.6 + - + +
113B TRP* 3.8 2.5 - - + -
147B PHE* 4.3 6.6 - - - -
1002B MBT 3.0 51.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 5.2 6.5 - - + -
101A ILE* 3.5 29.6 - - + -
152A ILE* 4.1 25.6 - - + -
92B VAL* 3.8 17.2 - - + +
93B SER 3.0 17.5 + - - +
94B ARG* 3.7 4.5 - - - +
96B GLU* 1.3 77.8 - - - +
98B LEU* 1.3 63.1 + - + +
100B LEU* 3.3 3.6 + - + +
101B ILE* 3.0 40.3 + - + +
148B VAL* 4.7 7.2 - - + -
151B TYR* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.2 24.9 - - + -
101A ILE* 4.6 22.4 - - + -
17B ILE* 3.7 32.5 - - + +
18B GLY* 4.6 0.7 - - - -
20B TYR 5.9 0.2 - - - +
21B SER* 5.7 2.7 - - - -
22B LEU* 3.9 12.4 - - + +
94B ARG* 3.0 49.7 + - + +
95B PRO* 3.9 3.8 - - + +
97B LEU* 1.3 76.2 - - + +
99B LEU* 1.3 62.4 + - - +
101B ILE* 3.4 5.6 + - + +
102B ASP* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.3 7.4 - - + -
17B ILE* 3.4 22.9 - - + -
22B LEU* 4.0 29.1 - - + +
52B LEU* 4.7 4.3 - - + -
55B MET* 4.2 24.5 - - + -
56B HIS* 3.1 41.7 - - + +
59B LEU* 3.6 27.8 - - + -
95B PRO 3.0 15.4 + - - +
96B GLU 3.7 3.4 - - - +
98B LEU* 1.3 75.8 - - - +
100B LEU* 1.3 59.4 + - - +
102B ASP* 3.0 4.0 + - + +
103B ALA 2.8 25.6 + - - -
113B TRP* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR 3.2 17.3 - - - +
152A ILE* 3.7 33.2 - - + +
153A HIS* 5.8 1.5 - - - +
92B VAL* 4.8 0.4 - - + -
96B GLU* 2.9 37.7 + - + +
97B LEU* 3.7 6.5 - - - +
99B LEU* 1.3 76.4 - - - +
101B ILE* 1.3 63.2 + - - +
103B ALA* 3.4 6.8 + - + +
104B PRO* 3.3 17.3 - - - +
113B TRP* 3.6 39.7 - - + +
147B PHE* 4.4 8.3 - - + -
1002B MBT 3.9 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.8 38.4 - - + +
97A LEU* 3.6 27.6 - - + -
98A LEU* 4.2 17.3 - - + -
101A ILE* 3.4 33.4 - - + -
151A TYR* 3.7 27.3 - - + +
97B LEU* 3.0 28.0 + - + +
98B LEU* 3.7 7.2 - - - +
99B LEU 3.2 0.2 - - - -
100B LEU* 1.3 76.1 - - - +
102B ASP* 1.3 58.8 + - - +
104B PRO* 3.3 13.2 - - - +
105B SER 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 4.8 15.3 + - - +
22B LEU* 3.6 26.5 - - + +
23B GLU* 5.0 5.7 - - - +
52B LEU* 4.7 10.9 - - - +
56B HIS* 4.7 5.7 + - + +
98B LEU 3.1 16.0 + - - +
99B LEU* 3.0 6.5 + - - +
101B ILE* 1.3 77.1 - - - +
103B ALA* 1.3 60.9 + - - +
104B PRO 3.3 1.1 - - - -
105B SER* 2.7 43.8 + - - -
109B PHE* 4.2 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 3.7 13.4 - - + -
99B LEU 2.8 11.8 + - - +
100B LEU* 3.7 9.9 - - + +
102B ASP* 1.3 77.3 - - - +
104B PRO* 1.3 65.1 - - + +
105B SER 2.9 6.6 + - - -
106B HIS 3.1 21.7 + - - +
109B PHE* 3.4 17.2 - - + +
110B LEU* 3.7 15.8 - - + +
113B TRP* 4.1 16.2 - - + +
----------------------------------------------------------
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