Contacts of the helix formed by residues 76 - 87 (chain A) in PDB entry 2YVL
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 TYR 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.9 14.1 - - + -
70A ARG* 3.6 25.6 + - - -
73A GLN* 3.1 31.4 + - - -
74A ILE* 3.6 30.2 - - + +
75A ILE* 1.3 74.6 - - - +
77A PRO* 1.4 62.2 - - + +
78A LYS* 3.1 10.3 - - + +
79A ASP* 2.8 29.5 + - - +
80A SER* 2.9 11.2 + - - -
237A THR* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.7 45.3 - - + +
64A ILE* 4.1 22.7 - - + -
65A LEU* 3.4 27.8 - - + -
75A ILE 4.1 0.2 - - - +
76A TYR* 1.4 83.1 - - + +
78A LYS* 1.3 58.8 + - - +
80A SER* 3.1 12.3 - - - +
81A PHE* 2.8 50.1 + - + +
82B TYR* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 5.2 0.4 + - - -
76A TYR* 4.4 6.9 - - + +
77A PRO* 1.3 78.2 - - - +
79A ASP* 1.3 74.7 + - - +
81A PHE* 5.1 0.7 - - - +
82A TYR* 4.2 6.4 + - - +
215A ILE* 2.8 57.1 + - + +
216A LEU* 5.2 0.4 - - - +
217A HIS* 3.7 51.1 + - + +
234A VAL* 4.7 15.0 - - + +
236A HIS* 5.8 0.6 - - - +
237A THR* 2.9 45.6 + - - +
238A ALA 5.6 0.4 + - - -
82B TYR* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.0 13.1 - - + +
76A TYR 2.8 16.0 + - - +
78A LYS* 1.3 95.1 + - - +
80A SER* 1.3 59.4 + - - +
81A PHE 3.3 0.4 - - - -
82A TYR* 3.2 5.7 + - - +
83A ILE* 2.9 37.6 + - + +
189A LEU* 4.3 10.4 - - + +
215A ILE* 3.9 17.9 + - - +
237A THR* 2.5 31.4 + - - +
238A ALA 4.4 3.2 + - - +
240A LEU* 4.0 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 5.0 0.3 - - - +
75A ILE* 3.9 10.4 + - - +
76A TYR 2.9 9.7 + - - -
77A PRO* 3.1 24.4 - - - +
79A ASP* 1.3 78.0 - - - +
81A PHE* 1.3 63.4 + - - +
83A ILE* 3.7 3.7 - - - +
84A ALA* 3.1 27.2 + - - +
104A ALA 4.7 0.9 + - - -
105A LEU* 3.6 32.3 - - - +
108A VAL* 3.3 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 13.9 - - + -
61A GLU* 3.8 34.5 - - + -
64A ILE* 4.7 0.4 - - + -
77A PRO* 2.8 35.8 + - + +
78A LYS 5.1 0.4 - - - +
80A SER* 1.3 77.9 - - - +
82A TYR* 1.3 62.2 + - - +
85A LEU* 3.9 11.8 + - - +
108A VAL* 3.8 23.6 - - + -
81B PHE 3.9 13.8 - - - +
82B TYR* 3.6 35.9 - + + -
85B LEU* 3.5 45.1 - - + +
86B LYS* 3.5 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS 4.2 4.5 + - - +
79A ASP 3.2 8.3 + - - +
81A PHE* 1.3 77.8 - - - +
83A ILE* 1.3 54.7 + - - +
85A LEU 3.3 2.3 + - - -
86A LYS* 2.8 56.2 + - + +
211A GLU* 5.1 0.7 + - - -
213A VAL* 4.3 12.4 - - + +
215A ILE* 3.7 27.6 - - + -
240A LEU* 4.5 2.0 - - + -
242A PHE* 3.8 28.9 - + - -
61B GLU* 2.6 31.5 + - - -
77B PRO 4.5 6.7 - - - -
78B LYS* 4.7 4.3 - - - +
81B PHE* 3.7 32.6 - + + -
82B TYR* 5.1 2.8 - - + +
217B HIS* 3.6 28.2 + + + +
219B HIS* 5.1 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.2 13.5 - - + -
79A ASP* 2.9 36.3 + - + +
80A SER* 3.3 10.3 + - - +
82A TYR* 1.3 73.1 - - - +
84A ALA* 1.3 59.2 - - - +
86A LYS* 3.3 1.2 + - - +
87A LEU* 2.9 43.3 + - + +
105A LEU* 4.1 13.9 - - + -
109A LEU* 4.8 1.1 - - + -
163A PHE* 3.6 46.9 - - + -
189A LEU* 4.7 0.2 - - + -
240A LEU* 4.2 13.2 - - + -
242A PHE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 3.1 16.2 + - - +
81A PHE 4.4 2.9 - - - +
82A TYR 3.3 0.4 + - - -
83A ILE* 1.3 78.0 - - - +
85A LEU* 1.3 61.5 + - - +
87A LEU* 3.9 1.4 + - - -
89A LEU* 3.3 33.2 + - + +
108A VAL* 3.7 21.3 - - + +
109A LEU* 4.2 22.7 - - + -
112A VAL* 4.0 20.1 - - + +
85B LEU* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 3.9 2.4 + - - +
82A TYR 3.3 2.3 + - - +
83A ILE 3.3 0.2 - - - -
84A ALA* 1.3 74.6 - - - +
86A LYS* 1.3 61.4 + - - +
87A LEU 3.2 1.6 - - - -
88A ASN* 2.9 21.3 + - - +
89A LEU 4.1 8.7 - - - +
112A VAL* 4.1 17.7 - - + -
59B THR* 5.6 0.2 - - - -
60B LEU* 4.5 21.3 + - + +
61B GLU 5.3 0.9 + - - -
81B PHE* 3.6 60.9 - - + +
84B ALA* 4.6 0.7 - - + -
85B LEU* 4.0 18.2 - - + -
108B VAL* 3.8 15.0 - - + -
111B GLU* 5.0 4.5 - - + -
112B VAL* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 2.8 48.6 + - + +
83A ILE 3.7 3.1 - - - +
85A LEU* 1.3 76.9 - - - +
87A LEU* 1.3 57.2 + - - +
88A ASN* 3.2 4.9 + - - -
185A PRO* 4.8 2.8 - - - +
211A GLU* 2.7 35.2 + - - -
242A PHE* 3.7 44.9 - - + -
18B LYS* 3.9 4.9 - - - +
59B THR* 4.3 19.8 + - - +
61B GLU* 2.8 33.9 + - + +
62B GLU* 5.0 2.2 + - - +
81B PHE* 3.6 7.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 2.9 38.6 + - + +
84A ALA 4.0 5.8 - - - +
85A LEU 3.2 0.2 - - - -
86A LYS* 1.3 71.6 - - - +
88A ASN* 1.3 68.9 + - - +
89A LEU* 3.3 20.9 + - + +
95A VAL* 4.8 1.8 - - + -
109A LEU* 4.4 5.4 - - + -
160A HIS 4.7 1.0 - - - +
161A ALA* 3.8 18.0 - - + +
162A ALA 3.7 15.9 - - - +
163A PHE* 4.1 10.8 - - + -
185A PRO* 3.7 27.4 - - + +
186A VAL* 3.7 11.2 - - - +
187A GLY* 3.6 29.6 - - - +
242A PHE* 4.3 7.6 - - + -
----------------------------------------------------------
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