Contacts of the helix formed by residues 59 - 68 (chain B) 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 THR 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 5.6 0.4 - - - -
86A LYS* 4.3 16.7 + - - +
88A ASN* 3.7 30.5 - - + +
185A PRO* 4.2 10.8 - - + -
244A ARG* 3.7 29.8 - - - +
58B PRO* 1.3 75.3 - - - +
60B LEU* 1.3 67.0 + - - +
61B GLU* 3.7 8.5 + - - +
62B GLU* 2.8 30.3 + - - +
63B ILE* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.5 17.3 - - + +
88A ASN* 2.8 21.4 + - - +
59B THR* 1.3 71.0 - - - +
61B GLU* 1.3 63.2 + - - +
63B ILE* 3.2 11.0 + - + +
64B ILE* 3.0 46.1 + - + +
81B PHE* 3.9 23.8 - - + -
107B ALA* 4.1 11.9 - - + +
108B VAL* 4.3 12.1 - - + -
111B GLU* 4.1 26.2 - - + +
138B LEU* 4.1 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 2.6 36.7 + - - -
85A LEU 5.3 0.6 + - - -
86A LYS* 2.8 34.5 + - + -
211A GLU* 4.1 5.0 - - - +
18B LYS* 4.5 5.0 + - - -
59B THR* 3.2 8.6 + - - +
60B LEU* 1.3 79.8 - - - +
62B GLU* 1.3 57.2 + - - +
64B ILE* 3.8 2.1 - - - +
65B LEU* 2.9 49.8 + - + +
77B PRO* 3.8 19.5 - - + +
78B LYS 5.3 0.2 + - - -
81B PHE* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 5.0 1.2 + - - -
209A ASN* 3.2 18.4 + - - -
211A GLU* 4.6 0.2 - - - +
244A ARG* 3.5 10.2 + - - -
11B LEU* 3.5 27.5 - - + +
18B LYS* 2.7 36.0 + - + +
20B LEU* 4.8 1.6 - - - +
58B PRO* 3.2 15.7 - - + +
59B THR* 2.8 38.5 + - - +
61B GLU* 1.3 77.6 - - + +
63B ILE* 1.3 60.2 + - - +
65B LEU* 4.6 4.7 - - - -
66B LEU* 2.9 36.7 + - + +
67B GLY 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 5.2 2.2 - - + -
58B PRO* 3.8 32.3 - - + +
59B THR 2.9 20.1 + - - +
60B LEU* 3.5 12.1 - - + +
62B GLU* 1.3 76.1 - - - +
64B ILE* 1.3 59.0 + - + +
67B GLY* 2.7 29.0 + - - +
68B PHE* 3.0 35.2 + - + -
136B PHE* 3.6 44.0 - - + +
138B LEU* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.0 40.3 + - + +
61B GLU 3.8 4.3 - - - +
63B ILE* 1.3 78.7 - - + +
65B LEU* 1.3 63.0 + - - +
66B LEU 3.5 0.2 + - - -
68B PHE* 3.5 31.1 + - + +
70B ARG* 4.6 3.5 + - - -
74B ILE* 4.5 10.8 - - + +
75B ILE 4.5 0.7 - - - +
77B PRO* 4.1 28.7 - - + -
80B SER* 5.0 0.4 - - - +
81B PHE* 4.4 1.6 - - + -
104B ALA* 3.8 36.1 - - + +
107B ALA* 4.4 8.1 - - + -
108B VAL* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 2.9 44.1 + - + +
62B GLU* 4.3 3.4 - - - +
64B ILE* 1.3 78.9 - - + +
66B LEU* 1.3 71.0 + - + +
68B PHE 5.4 0.9 - - - +
70B ARG* 2.8 29.8 + - - +
74B ILE* 4.8 0.4 - - + -
76B TYR* 3.7 23.6 - - + -
77B PRO* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.8 29.6 - - + -
18B LYS* 4.0 26.5 - - + +
19B PHE* 4.2 0.9 - - - -
20B LEU* 3.8 33.3 - - + +
62B GLU* 2.9 21.3 + - + +
65B LEU* 1.3 84.9 - - + +
67B GLY* 1.3 58.4 + - - +
68B PHE 3.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.6 18.3 - - - +
62B GLU 3.7 1.4 + - - -
63B ILE 2.7 18.6 + - - -
66B LEU* 1.3 75.5 - - - +
68B PHE* 1.3 62.4 + - - +
69B GLU* 3.5 2.4 + - - +
132B ASN* 4.5 1.2 - - - +
135B LYS* 4.5 9.5 + - - +
136B PHE* 3.9 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.0 36.5 + - + -
64B ILE* 3.5 23.5 + - + +
65B LEU 5.4 0.3 - - - +
66B LEU 5.1 1.6 - - - -
67B GLY* 1.3 78.7 + - - +
69B GLU* 1.3 64.2 + - - +
70B ARG* 3.5 16.1 + - + +
74B ILE* 6.0 2.0 - - + -
102B SER* 4.0 6.7 - - - -
103B GLY 3.3 25.1 - - - -
104B ALA* 4.0 15.3 - - + -
107B ALA* 3.9 17.3 - - + -
132B ASN* 3.5 41.3 - - + +
133B LEU* 3.7 23.3 - - + -
136B PHE* 3.9 5.2 - + - -
138B LEU* 4.2 5.8 - - + -
----------------------------------------------------------
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