Contacts of the helix formed by residues 116 - 133 (chain A) in PDB entry 3V4R
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 ASN 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 2.6 22.4 + - - +
94A ASP* 3.1 36.1 + - - +
114A SER 3.9 1.2 + - - -
115A ILE* 1.3 70.5 - - - +
117A ASP* 1.3 63.1 + - - +
118A GLU* 3.1 23.4 + - - +
119A ILE* 3.3 30.0 + - + +
120A ASP* 3.2 16.5 + - - +
207A ARG* 5.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.6 15.4 + - - +
116A ASN* 1.3 70.6 + - - +
118A GLU* 1.4 57.5 + - - +
120A ASP* 3.3 21.3 + - - +
121A LYS* 3.0 27.5 + - - +
207A ARG* 3.7 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 3.1 11.7 + - - +
117A ASP* 1.4 72.5 - - - +
119A ILE* 1.4 61.4 + - + +
121A LYS* 3.4 11.6 + - - +
122A LEU* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.9 2.9 - - + +
88A TYR* 5.2 8.5 - - + +
90A VAL* 3.9 25.8 - - + +
91A SER 3.4 29.8 - - - +
92A TYR* 3.7 9.2 - - + +
93A TYR 5.7 0.4 - - - +
94A ASP* 4.3 6.1 - - - +
116A ASN* 3.3 39.6 + - + +
118A GLU* 1.4 73.7 - - + +
120A ASP* 1.3 60.2 + - - +
122A LEU* 3.1 18.5 + - + +
123A ARG* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.3 35.8 - - + +
115A ILE* 4.8 5.2 - - + +
116A ASN 3.2 12.2 + - - +
117A ASP* 3.4 25.0 - - - +
119A ILE* 1.3 76.0 - - - +
121A LYS* 1.4 60.2 + - - +
123A ARG* 3.3 10.0 + - - +
124A HIS* 3.1 53.9 + - - -
7D T 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP 3.0 12.7 + - - +
118A GLU* 3.4 12.6 - - - +
119A ILE 3.3 0.2 - - - -
120A ASP* 1.4 73.7 + - - +
122A LEU* 1.4 58.2 + - + +
124A HIS* 3.3 12.3 + - - +
125A SER* 3.0 34.4 + - - +
207A ARG 5.7 0.8 + - - -
208A ASP* 5.1 12.5 - - - +
210A HIS* 6.0 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 4.6 14.8 - - + +
87A GLU* 4.3 4.3 - - - +
88A TYR* 3.4 51.2 + - + +
118A GLU* 3.1 21.2 + - + +
119A ILE* 3.1 19.2 + - + +
121A LYS* 1.4 75.9 - - + +
123A ARG* 1.4 58.7 + - - +
125A SER* 3.4 11.3 + - - +
126A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR 4.2 2.7 - - - +
89A PHE* 3.3 46.8 - - + -
90A VAL 2.8 44.6 + - - +
91A SER* 3.9 4.8 - - - +
92A TYR* 3.9 32.4 - - - +
119A ILE* 2.9 18.6 + - + +
120A ASP* 3.3 9.7 + - - +
122A LEU* 1.4 74.1 - - - +
124A HIS* 1.4 61.2 + - + +
126A ALA* 3.3 3.8 + - - +
127A THR* 3.0 30.4 + - - +
143A SER* 3.0 22.0 + - - -
148A LEU* 4.7 7.3 - - - +
7D T 3.4 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASP* 3.1 47.0 + - - -
121A LYS* 3.4 11.4 - - - +
123A ARG* 1.4 76.6 - - + +
125A SER* 1.4 54.6 + - - +
127A THR* 3.6 5.2 - - - -
128A SER* 2.5 39.1 + - - -
154A TYR* 3.2 10.3 + + - -
244A PHE* 3.5 56.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.4 19.3 - - - +
121A LYS* 3.0 20.6 + - - +
122A LEU* 3.5 13.3 - - - +
123A ARG 3.3 0.2 - - - -
124A HIS* 1.4 74.9 - - - +
126A ALA* 1.3 57.0 + - - +
128A SER* 3.8 4.7 + - - -
129A ALA* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.6 26.9 + - + -
88A TYR 4.3 4.7 - - - +
89A PHE* 4.2 20.4 - - + -
122A LEU 3.1 12.9 + - - +
123A ARG* 3.3 10.5 - - - +
125A SER* 1.3 73.5 - - - +
127A THR* 1.4 64.4 + - - +
129A ALA* 3.2 16.5 + - - +
130A LEU* 3.4 4.7 + - - +
138A ILE* 4.1 20.3 - - + +
325A LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 4.1 10.3 - - + -
123A ARG 3.0 20.2 + - - +
124A HIS* 3.4 5.4 + - - -
126A ALA* 1.4 71.1 - - - +
128A SER* 1.4 58.8 + - - +
130A LEU* 3.2 17.4 + - - +
131A PHE* 3.3 15.7 - - - -
148A LEU* 4.2 10.1 - - + -
154A TYR* 2.8 35.5 + - + -
325A LEU* 3.6 27.4 - - + -
328A TYR* 4.0 21.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS 2.5 24.1 + - - -
125A SER* 3.8 5.2 + - - -
127A THR* 1.4 73.6 - - - +
129A ALA* 1.4 61.8 + - - +
131A PHE* 3.3 17.3 + - - +
132A GLU* 3.5 24.9 + - - +
154A TYR* 3.2 24.4 + - - -
244A PHE* 4.6 8.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 4.5 7.4 - - + -
87A GLU* 4.0 20.6 - - + +
125A SER 3.1 21.7 + - - +
126A ALA 3.2 7.8 + - - +
128A SER* 1.4 76.3 + - - +
130A LEU* 1.3 57.3 + - - +
132A GLU* 3.9 11.4 + - - +
133A ARG* 3.2 33.7 + - + +
136A VAL* 3.7 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 4.7 7.2 - - + -
126A ALA 3.4 2.8 + - - +
127A THR 3.2 11.9 + - - +
129A ALA* 1.3 77.9 - - - +
131A PHE* 1.4 60.2 + - + +
133A ARG 4.0 10.4 - - - +
136A VAL* 4.1 20.2 - - + -
138A ILE* 3.8 20.4 - - + -
325A LEU* 4.4 7.2 - - + -
328A TYR* 3.6 46.1 - - + +
329A PHE* 3.7 44.0 - - + -
330A PRO* 4.8 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR 3.3 19.3 - - - -
128A SER* 3.3 13.3 + - - +
129A ALA 3.2 0.8 - - - -
130A LEU* 1.4 77.4 - - + +
132A GLU* 1.3 68.3 + - + +
151A PRO* 3.7 35.0 - - + -
154A TYR* 3.4 27.8 - + - -
155A ARG* 5.0 10.3 - - + -
328A TYR* 3.5 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 3.5 23.2 + - - +
129A ALA* 3.4 13.0 + - - +
131A PHE* 1.3 80.2 - - + +
133A ARG* 1.3 65.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 3.6 8.3 - - - +
59A PRO* 5.6 0.2 - - - +
83A ASN 3.7 9.9 + - - -
84A ASN* 3.7 8.3 - - - +
85A ALA* 3.6 35.5 - - + +
129A ALA* 3.2 14.3 + - + +
130A LEU* 4.0 11.1 - - - +
131A PHE 3.8 0.2 - - - -
132A GLU* 1.3 84.2 + - + +
134A ARG* 1.3 60.0 + - - +
135A ASP* 2.6 47.8 + - - +
136A VAL* 3.2 19.3 - - + +
----------------------------------------------------------
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