Contacts of the helix formed by residues 121 - 135 (chain B) in PDB entry 2VE7
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 121 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS* 4.0 27.8 + - - +
200A GLU* 3.1 17.7 - - - -
119B ALA 3.6 1.0 + - - -
120B PRO* 1.3 77.1 - - - +
122B VAL* 1.3 61.8 + - - +
123B LYS* 3.5 6.0 + - - +
124B ASP* 2.9 34.4 + - - +
125B PHE* 2.9 21.0 + - - +
172B VAL* 4.6 0.9 - - - -
2225B GOL 4.1 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLU* 2.4 34.6 + - + +
121B SER* 1.3 66.0 - - - +
123B LYS* 1.3 62.3 + - - +
125B PHE* 3.3 2.7 + - + +
126B LEU* 2.9 36.6 + - + +
147B PHE* 3.6 29.4 - - + -
169B MET 3.6 13.9 - - - +
170B TYR* 3.6 25.1 - - - +
172B VAL* 3.8 13.0 - - + -
2225B GOL 3.8 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS 5.6 1.1 - - - +
200A GLU* 3.4 32.7 + - + +
202A SER* 4.9 17.0 - - - +
121B SER* 3.7 8.3 - - - +
122B VAL* 1.3 80.1 - - - +
124B ASP* 1.3 64.8 + - - +
126B LEU* 3.5 8.2 + - - +
127B LYS* 3.3 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 4.3 0.8 + - - -
116B SER* 5.1 4.9 - - - +
120B PRO* 4.1 11.3 - - + +
121B SER* 2.9 32.0 + - - +
123B LYS* 1.3 77.9 - - - +
125B PHE* 1.3 67.2 + - - +
127B LYS* 2.9 20.2 + - - +
128B ILE* 2.9 31.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
120B PRO* 4.5 7.9 - - + +
121B SER 2.9 12.0 + - - +
122B VAL* 3.5 7.0 - - - +
124B ASP* 1.3 75.0 - - - +
126B LEU* 1.3 75.9 + - + +
128B ILE* 3.1 9.5 + - - +
129B PHE* 2.7 42.2 + + + +
147B PHE* 5.4 1.6 - + - -
151B VAL* 4.0 27.8 - - + -
155B PHE* 5.3 2.5 - + - -
169B MET* 4.4 9.9 - - + -
172B VAL* 3.7 32.8 - - + -
178B TRP* 4.6 4.9 - + - -
181B ILE* 3.4 31.2 - - + -
185B LEU* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 2.9 37.1 + - + +
123B LYS* 3.9 7.2 - - - +
124B ASP 3.1 0.4 - - - -
125B PHE* 1.3 90.2 - - + +
127B LYS* 1.3 59.0 + - + +
129B PHE* 4.1 3.7 - - + +
130B THR* 2.7 37.6 + - - -
142B LEU* 3.7 27.4 - - + -
147B PHE* 3.6 41.1 - - + -
151B VAL* 4.1 7.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
108B TYR* 3.1 18.1 - - + +
110B HIS* 3.5 37.8 + - + +
123B LYS* 3.3 47.5 + - - +
124B ASP* 2.9 17.3 + - - +
126B LEU* 1.3 75.7 - - - +
128B ILE* 1.3 56.1 + - - +
130B THR* 3.5 4.6 + - - -
131B PHE* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.1 13.9 - - + -
103B LEU* 3.9 13.5 - - + -
108B TYR* 3.5 24.9 - - + +
112B VAL* 5.0 3.6 - - + -
117B LEU* 3.8 29.2 - - + -
120B PRO* 5.3 4.7 - - + -
124B ASP* 2.9 24.7 + - + +
125B PHE* 3.5 9.9 - - - +
127B LYS* 1.3 75.0 - - - +
129B PHE* 1.3 66.1 + - - +
131B PHE* 3.2 3.1 + - - +
132B LEU* 3.0 34.4 + - + +
178B TRP* 5.7 2.5 - - + -
185B LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 2.7 34.5 + + + +
126B LEU* 4.1 4.0 - - - +
128B ILE* 1.3 74.6 - - - +
130B THR* 1.3 66.7 + - - +
132B LEU* 3.3 3.4 + - - +
133B TYR* 2.9 39.9 + + + +
140B TYR* 4.3 16.4 - + - -
142B LEU* 4.7 7.6 - - + -
151B VAL* 3.9 29.4 - - + -
154B ILE* 3.9 37.9 - - + -
155B PHE* 3.6 33.2 - + - -
158B LEU* 6.2 0.4 - - + -
185B LEU* 4.5 9.2 - - + -
188B LEU* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU 2.7 23.5 + - - -
127B LYS* 3.8 5.4 - - - -
129B PHE* 1.3 82.5 - - - +
131B PHE* 1.3 62.0 + - - +
133B TYR* 4.0 3.2 - - - +
134B GLY* 3.1 20.4 + - - -
140B TYR* 3.4 32.2 - - + +
141B GLU* 4.4 7.6 - - + -
142B LEU* 3.6 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.6 3.1 - + - -
103B LEU* 3.5 29.6 - - + -
106B ASN* 3.4 32.1 - - + -
107B GLY 4.6 2.0 - - - -
108B TYR* 3.4 38.4 - + + -
109B ALA 5.2 0.4 - - - -
127B LYS 3.0 17.9 + - - +
128B ILE 3.5 4.3 - - - +
129B PHE 3.2 0.2 - - - -
130B THR* 1.3 77.1 - - - +
132B LEU* 1.3 67.3 + - + +
134B GLY* 3.1 13.0 + - - -
135B PHE* 3.3 40.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.1 11.2 - - + -
102B PHE* 3.5 38.4 - - + -
103B LEU* 4.2 12.8 - - + -
128B ILE* 3.0 30.7 + - + +
129B PHE* 3.8 1.3 - - - +
131B PHE* 1.3 77.3 - - + +
133B TYR* 1.3 63.5 + - - +
135B PHE* 3.1 26.0 + - - +
136B LEU* 4.2 0.9 + - - +
185B LEU* 4.0 38.8 - - + +
188B LEU* 3.7 16.2 - - + -
189B ILE* 4.0 10.1 - - + -
192B ILE* 3.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 2.9 31.9 + + + +
130B THR 4.2 2.7 - - - +
132B LEU* 1.3 77.6 - - - +
134B GLY* 1.3 54.0 + - - +
136B LEU* 2.8 39.3 + - + +
137B CYS* 2.8 25.8 + - - -
140B TYR* 3.5 42.8 - + + -
154B ILE* 3.4 47.3 - - + +
158B LEU* 4.2 14.8 - - + -
188B LEU* 4.3 6.9 - - + +
110D LEU* 3.2 33.7 - - + +
111D CYS* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR 3.1 15.3 + - - -
131B PHE 3.1 7.7 + - - -
133B TYR* 1.3 74.4 - - - +
135B PHE* 1.3 63.1 + - - +
136B LEU 3.1 1.1 + - - -
137B CYS 3.3 14.3 - - - -
138B PRO* 3.4 23.8 - - - +
139B SER 4.5 1.2 + - - -
140B TYR* 4.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.1 9.6 - + - -
106B ASN* 3.8 40.8 - - + -
131B PHE* 3.3 45.5 - + - -
132B LEU* 3.1 15.3 + - - +
133B TYR 3.1 0.4 - - - -
134B GLY* 1.3 76.9 - - - +
136B LEU* 1.3 62.7 + - - +
138B PRO* 5.1 2.8 - - - +
192B ILE* 3.9 33.8 - - + +
195B HIS* 4.9 5.4 - - - -
196B THR* 5.8 1.3 - - - -
199B LYS* 5.8 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