Contacts of the helix formed by residues 99 - 111 (chain A) in PDB entry 5LPN
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 99 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 2.7 36.3 + - - +
95A LYS* 3.0 48.9 + - - +
96A SER 3.9 2.2 - - - +
97A PHE 3.2 0.8 - - - -
98A GLU* 1.3 76.5 - - - +
100A ILE* 1.3 63.8 + - - +
101A SER* 3.1 4.0 - - - -
102A LYS* 3.1 30.4 + - - +
103A TRP* 3.0 24.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.3 15.7 - - + -
88A VAL 4.3 8.3 - - - +
89A TYR* 4.1 20.6 - - + -
96A SER 3.6 8.2 + - - +
97A PHE* 3.5 26.2 - - + +
98A GLU 3.3 1.6 - - - -
99A ASN* 1.3 76.3 - - - +
101A SER* 1.3 64.4 + - - +
103A TRP* 3.3 9.3 + - + +
104A LEU* 2.9 43.8 + - + +
119A LEU* 3.7 35.0 - - + -
140A ILE* 5.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU 3.4 17.0 + - - -
99A ASN* 4.6 0.3 - - - -
100A ILE* 1.3 79.4 - - - +
102A LYS* 1.3 61.8 + - - +
104A LEU* 3.4 12.8 + - - +
105A ARG* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 5.0 4.6 + - - -
69A GLU* 4.8 15.2 + - - +
99A ASN* 3.1 38.5 + - - +
101A SER* 1.3 79.1 + - - +
103A TRP* 1.3 81.2 + - - +
105A ARG* 3.1 19.0 + - + +
106A ASN* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.0 16.7 - - + +
16A GLY* 3.3 38.4 - - - -
17A ASP* 2.1 37.1 + - - +
65A THR* 6.0 0.7 - - - -
66A ALA 4.9 4.9 - - - -
67A GLY* 4.0 16.2 - - - -
69A GLU* 6.3 1.8 - - - -
72A HIS* 5.5 9.4 - + + -
75A THR* 5.6 5.2 - - - -
76A THR* 6.0 0.2 - - + -
79A TYR* 3.8 18.2 - - - -
87A LEU* 3.8 17.5 - - + -
88A VAL 5.2 0.2 - - - -
96A SER 5.1 1.3 - - - -
99A ASN* 3.0 30.6 + - - +
100A ILE* 3.6 14.4 - - + +
102A LYS* 1.3 87.7 - - - +
104A LEU* 1.3 64.2 + - - +
106A ASN* 3.0 43.7 + - - +
107A ILE* 3.0 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.5 30.5 - - + +
100A ILE* 2.9 36.8 + - + +
101A SER* 3.7 9.4 - - - +
103A TRP* 1.3 75.3 - - - +
105A ARG* 1.3 56.8 - - - +
107A ILE* 3.1 9.5 + - + +
108A ASP* 2.9 31.3 + - - +
117A ARG* 3.8 25.4 + - - +
140A ILE* 5.2 1.1 - - + -
144A HIS* 3.9 40.2 - - + +
146A ILE* 4.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER 3.0 14.6 + - - +
102A LYS* 3.1 24.1 + - + +
104A LEU* 1.3 74.3 - - - +
106A ASN* 1.3 68.5 + - - +
108A ASP* 3.1 12.4 + - - +
109A GLU* 2.8 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 3.5 27.6 + - - -
76A THR* 4.3 6.1 - - + -
79A TYR* 3.6 16.6 + - + +
102A LYS* 3.0 30.5 + - - +
103A TRP* 3.1 41.5 - - - +
105A ARG* 1.3 81.2 - - - +
107A ILE* 1.3 58.1 + - - +
109A GLU* 4.2 6.7 - - - +
110A HIS* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.6 31.4 - - + -
79A TYR* 3.9 8.5 - - + -
85A ILE* 3.8 21.3 - - + -
87A LEU* 3.6 31.9 - - + -
103A TRP 3.0 7.6 + - - +
104A LEU* 3.2 8.7 - - + +
106A ASN* 1.3 77.5 - - - +
108A ASP* 1.3 58.8 + - - +
111A ALA* 2.7 44.7 + - + +
112A ASN 5.0 0.3 - - - +
115A VAL* 4.2 6.7 - - + -
117A ARG* 3.3 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.9 19.3 + - - +
105A ARG* 3.1 13.7 + - - +
107A ILE* 1.3 76.2 - - - +
109A GLU* 1.3 64.1 + - + +
111A ALA 4.5 4.9 - - - +
117A ARG* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 2.8 41.8 + - + +
106A ASN* 3.6 2.7 - - - +
108A ASP* 1.3 79.5 - - + +
110A HIS* 1.3 90.9 + - + +
111A ALA 4.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 4.7 10.5 - + - -
76A THR* 3.6 48.1 - - + +
79A TYR* 3.2 22.5 + - + +
80A ARG* 3.8 6.6 + - - +
106A ASN* 2.8 16.4 + - - +
109A GLU* 1.3 108.6 + - + +
111A ALA* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.7 18.7 - - + +
80A ARG* 5.2 0.7 - - - -
85A ILE* 4.2 8.3 - - + -
107A ILE* 2.7 43.8 + - + +
108A ASP 4.5 4.7 - - - +
109A GLU 4.8 1.0 - - - +
110A HIS* 1.3 77.6 + - - +
112A ASN* 1.3 74.6 + - - +
113A GLU 3.7 0.9 + - - -
115A VAL* 3.9 9.6 - - + -
----------------------------------------------------------
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