Contacts of the helix formed by residues 122 - 136 (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 VAL 122 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 3.0 14.0 + - - +
121B ALA* 1.3 79.9 - - + +
123B GLU* 1.3 60.5 + - - +
124B GLU* 3.9 16.8 - - + +
125B PHE* 3.1 31.7 + - + +
126B TYR* 3.0 24.6 + - - +
146B ASN* 3.7 0.9 - - - -
602B SAM 3.5 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ALA 3.5 4.8 + - - -
122B VAL* 1.3 71.8 - - - +
124B GLU* 1.3 63.9 + - - +
126B TYR* 3.4 4.2 - - + +
127B LYS* 3.0 51.5 + - + +
146B ASN* 3.4 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.4 28.6 - - - +
122B VAL* 3.3 8.6 - - + +
123B GLU* 1.3 78.0 - - - +
125B PHE* 1.3 78.2 + - + +
127B LYS* 3.4 7.3 + - - +
128B THR* 2.8 34.8 + - - +
131B LYS* 5.2 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.7 37.7 - - + -
72B THR* 3.6 14.4 - - + -
101B GLY 3.1 24.9 - - - +
120B GLU* 3.8 8.7 - - - +
122B VAL* 3.1 34.6 + - + +
124B GLU* 1.3 100.0 - - + +
126B TYR* 1.3 60.8 + - - +
128B THR* 3.2 5.0 + - - -
129B ALA* 2.9 28.2 + - - +
602B SAM 3.3 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 5.6 0.9 - - - -
120B GLU* 3.5 14.6 - - + +
122B VAL 3.0 13.8 + - - +
123B GLU* 3.4 13.5 - - + +
125B PHE* 1.3 76.3 - - - +
127B LYS* 1.3 82.7 + - + +
129B ALA* 4.0 4.7 - - - +
130B GLN* 3.1 53.4 + - - +
144B PHE* 3.7 30.9 + + + +
145B PHE 3.9 6.3 - - - -
146B ASN* 3.6 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU* 3.0 40.5 + - + +
124B GLU* 3.7 7.9 - - - +
126B TYR* 1.3 96.6 - - + +
128B THR* 1.3 59.1 + - - +
130B GLN* 3.3 11.5 + - - +
131B LYS* 2.9 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 3.8 38.1 + - + +
71B LYS* 3.9 29.9 - - + +
101B GLY 5.1 0.7 - - - -
102B SER* 4.6 5.4 - - - +
124B GLU* 2.8 26.0 + - - +
125B PHE* 3.2 9.6 + - - -
127B LYS* 1.3 75.6 - - - +
129B ALA* 1.3 56.5 + - - +
131B LYS* 3.3 17.1 + - + +
132B ASN* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 3.5 31.6 - - + -
101B GLY 3.6 7.4 + - - +
102B SER 3.5 17.0 - - - -
103B GLY* 3.9 2.7 - - - +
106B LEU* 4.8 0.4 - - + -
125B PHE 2.9 20.4 + - - +
126B TYR 4.0 4.5 - - - +
128B THR* 1.3 73.2 - - - +
130B GLN* 1.3 62.1 + - - +
132B ASN* 3.4 0.5 + - - +
133B LEU* 3.2 30.5 + - - +
144B PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.1 52.3 + - - +
127B LYS* 3.3 15.2 + - - +
129B ALA* 1.3 78.5 - - - +
131B LYS* 1.3 57.6 - - + +
133B LEU* 4.0 0.7 - - - +
134B LYS* 2.9 48.0 + - - +
144B PHE* 3.5 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 5.4 10.5 + - - +
124B GLU* 5.2 1.2 + - - +
127B LYS* 2.9 44.4 + - - +
128B THR* 3.7 15.9 + - + +
130B GLN* 1.3 75.9 - - + +
132B ASN* 1.3 63.4 + - - +
134B LYS* 4.0 11.1 - - - +
135B LYS* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY 4.5 1.2 - - - +
68B PHE* 3.5 31.1 - - + +
69B GLU* 2.9 52.8 + - - +
102B SER 2.8 25.0 + - - +
128B THR* 2.8 23.0 + - - +
129B ALA 3.6 4.9 - - - +
131B LYS* 1.3 76.5 - - - +
133B LEU* 1.3 62.5 + - - +
135B LYS* 3.5 6.8 + - - +
136B PHE* 3.4 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.7 17.0 - - + -
103B GLY* 3.4 31.0 - - - +
106B LEU* 4.0 23.8 - - + -
107B ALA* 3.9 20.0 - - + -
110B SER* 4.5 2.2 - - - -
129B ALA 3.2 25.6 + - - +
130B GLN 4.3 1.3 - - - +
132B ASN* 1.3 77.0 - - + +
134B LYS* 1.3 62.4 + - - +
136B PHE 3.1 8.5 + - - -
138B LEU* 2.8 44.5 + - + +
139B GLY* 3.8 26.0 - - - +
144B PHE* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLN* 2.9 34.8 + - - +
131B LYS* 4.0 9.6 - - - +
133B LEU* 1.3 75.3 - - - +
135B LYS* 1.3 62.0 + - - +
137B ASN* 3.1 14.5 + - - +
138B LEU 4.1 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.1 48.5 + - + -
67B GLY* 4.5 10.0 + - - +
131B LYS 3.1 17.9 + - - +
132B ASN* 3.6 8.7 - - - +
133B LEU 3.3 0.2 - - - -
134B LYS* 1.3 77.9 - - - +
136B PHE* 1.3 84.5 + - + +
137B ASN 3.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 4.0 32.5 - + + -
20B LEU* 4.4 7.2 - - + -
58B PRO* 5.4 1.8 - - + -
63B ILE* 3.6 50.1 - - + +
67B GLY* 3.9 36.3 - - - -
68B PHE* 3.9 3.8 - + - -
132B ASN* 3.4 17.9 + - - +
133B LEU 3.1 5.1 + - - +
135B LYS* 1.3 107.9 - - + +
137B ASN* 1.3 69.4 + - - +
138B LEU* 3.3 18.2 + - + +
----------------------------------------------------------
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