Contacts of the helix formed by residues 115 - 129 (chain H) in PDB entry 1PV2
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 LYS 115 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 4.2 17.0 + - + +
39H VAL* 4.2 22.2 + - - +
83H TYR* 3.5 42.1 + - + +
113H ASP* 3.0 5.3 + - - +
114H GLU* 1.3 86.7 - - + +
116H VAL* 1.3 65.2 + - - +
117H MET 3.5 0.7 - - - -
118H PRO* 3.5 5.2 - - - +
119H PHE* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H SER* 2.8 26.2 - - - +
36H LEU* 4.3 16.2 - - + -
76H ILE* 5.4 0.7 - - + -
79H LEU* 4.0 31.0 - - + -
80H LEU* 3.9 14.6 - - + -
83H TYR* 4.8 4.7 - - + -
109H MET* 5.2 1.8 - - - -
110H PRO* 3.8 20.6 - - + -
113H ASP* 2.7 24.7 + - + +
115H LYS* 1.3 70.3 - - - +
117H MET* 1.3 66.7 + - - +
119H PHE* 3.2 8.5 + - + +
120H PHE* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H MET* 4.6 19.1 - - - +
110H PRO* 3.7 14.8 - - - +
111H HIS* 4.2 15.3 - - + -
112H LYS* 3.9 6.1 - - - +
113H ASP 3.1 31.9 + - - +
116H VAL* 1.3 78.9 - - - +
118H PRO* 1.3 65.9 - - + +
120H PHE* 3.1 11.6 + - + +
121H GLU* 2.8 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ASP 3.5 2.0 - - - +
114H GLU 3.0 28.9 - - - +
115H LYS* 3.5 9.0 - - - +
117H MET* 1.3 96.7 - - + +
119H PHE* 1.3 52.3 + - - +
121H GLU* 3.0 8.1 + - + +
122H GLN* 2.6 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LEU* 4.0 26.2 - - + -
82H LEU* 3.7 17.5 - - + -
83H TYR* 3.6 54.3 - + + -
86H HIS* 3.8 22.0 - + + -
92H PHE* 3.9 17.7 - + - -
115H LYS 3.3 12.0 + - - +
116H VAL* 3.2 10.0 + - + +
118H PRO* 1.3 78.0 - - - +
120H PHE* 1.3 63.9 + - - +
122H GLN* 3.6 8.4 - - - +
123H HIS* 3.0 59.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ASP* 4.1 8.5 - - - -
79H LEU* 3.8 30.1 - - + -
104H PHE* 3.6 24.9 - + - -
106H TYR* 3.6 29.2 - + - -
109H MET* 3.8 25.1 - - + -
116H VAL 2.9 13.5 + - - +
117H MET* 3.4 15.0 - - + +
119H PHE* 1.3 77.2 - - - +
121H GLU* 1.3 68.5 + - - +
123H HIS* 3.3 2.8 + - - -
124H LYS* 2.8 63.1 + - + +
127H PHE* 4.3 11.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ASP* 4.8 3.8 - - - +
117H MET* 2.8 35.4 + - + +
118H PRO* 3.5 10.3 - - + +
120H PHE* 1.3 95.1 - - - +
122H GLN* 1.3 63.3 + - + +
123H HIS 3.2 0.9 + - - -
124H LYS* 3.0 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN* 4.4 18.0 + - - +
118H PRO* 2.6 35.8 + - + +
119H PHE* 3.6 9.5 - - - +
121H GLU* 1.3 73.4 - - + +
123H HIS* 1.3 79.4 + - + +
124H LYS 3.6 0.4 + - - -
125H SER* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 3.9 24.7 + + - -
91H GLU* 4.5 7.9 + - - -
92H PHE* 3.7 24.0 - + + -
119H PHE* 3.0 59.6 + + + +
120H PHE* 3.5 2.2 - - - +
122H GLN* 1.3 95.3 + - + +
124H LYS* 1.3 66.0 + - - +
125H SER* 3.1 4.4 + - - -
126H LEU* 3.1 38.1 + - + +
127H PHE* 3.8 12.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ASP* 3.3 29.3 + - - +
17G ASN* 5.2 6.9 - - - +
120H PHE* 2.8 37.1 + - + +
121H GLU* 3.0 38.8 + - - +
122H GLN 3.6 0.4 - - - -
123H HIS* 1.3 77.6 - - - +
125H SER* 1.3 63.4 + - - +
127H PHE* 3.1 13.2 + - - +
128H ARG* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H GLU 5.1 0.2 + - - -
122H GLN 5.3 1.1 + - - -
123H HIS* 3.1 1.9 + - - -
124H LYS* 1.3 79.4 - - - +
126H LEU* 1.3 66.9 + - - +
128H ARG* 3.7 7.6 - - - +
129H ASN* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLU* 5.8 2.0 - - - +
92H PHE* 3.7 38.6 - - + +
93H GLU* 5.4 8.7 - - + -
94H VAL* 3.4 32.3 + - + +
123H HIS* 3.1 35.3 + - + +
125H SER* 1.3 85.7 - - - +
127H PHE* 1.3 61.5 + - - +
129H ASN 3.8 2.9 - - - +
130H PRO* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H VAL* 4.8 7.6 - - + -
55H ALA* 5.4 1.1 - - + -
78H THR* 3.9 20.9 - - - -
79H LEU* 3.8 19.5 - - + -
82H LEU* 4.0 20.2 - - + -
92H PHE* 4.0 16.2 - + - -
94H VAL* 3.5 26.0 - - + -
102H THR* 2.7 49.1 + - + +
104H PHE* 3.8 28.9 - + + -
120H PHE* 4.3 12.8 - + + -
123H HIS* 3.9 15.3 - - + -
124H LYS 3.1 6.6 + - - +
126H LEU* 1.3 76.7 - - - +
128H ARG* 1.3 63.3 + - + +
130H PRO* 3.3 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ASP* 3.5 26.3 + - - +
17G ASN* 4.1 7.9 - - - +
62G PRO* 5.3 4.7 - - - +
66G GLY* 2.9 31.9 + - - -
68G LEU* 4.1 26.1 - - - +
101H MET* 3.3 38.5 + - + +
102H THR 4.7 0.2 - - - +
124H LYS* 3.0 52.2 + - + +
125H SER* 3.3 7.2 + - - +
127H PHE* 1.3 80.0 - - + +
129H ASN* 1.3 73.9 + - - +
130H PRO* 3.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G PRO* 6.0 4.4 - - - +
125H SER* 2.9 25.4 + - - +
126H LEU* 3.8 7.5 - - - +
128H ARG* 1.3 92.5 + - - +
130H PRO* 1.3 66.7 - - - +
131H LYS* 5.5 0.7 - - - +
----------------------------------------------------------
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