Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 4LP8
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 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.7 5.6 - - - +
78A ALA* 5.9 0.3 - - - +
79A ARG* 3.1 56.1 + - - +
80A PRO 3.2 2.6 + - - -
81A GLY* 1.4 73.9 - - - +
83A PHE* 1.4 62.2 + - - +
84A THR* 3.8 4.5 + - - -
85A ASP* 3.5 16.4 + - - +
86A ALA* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.5 48.5 - - + -
65A ALA* 3.5 14.8 - - + -
66A LEU* 3.8 27.4 - - + -
69A LEU* 3.8 14.4 - - + -
81A GLY 3.4 5.6 + - - +
82A SER* 1.4 69.4 + - - +
84A THR* 1.4 60.1 - - - +
86A ALA* 3.1 3.4 + - - +
87A PHE* 2.7 51.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.3 10.1 - - - +
82A SER* 3.8 8.5 + - - -
83A PHE* 1.4 80.9 - - - +
85A ASP* 1.3 63.8 + - - +
87A PHE* 3.2 6.2 + - - +
88A PHE* 3.0 59.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 5.0 0.2 - - - -
77A ASN 4.2 2.4 - - - +
78A ALA* 3.3 24.5 - - + -
79A ARG* 2.7 63.5 + - - +
82A SER* 3.5 17.1 + - - +
83A PHE 3.4 0.4 - - - -
84A THR* 1.3 77.7 - - - +
86A ALA* 1.4 58.1 + - - +
88A PHE* 3.5 3.0 + - - -
89A PHE* 2.9 30.0 + - - +
102A LEU* 3.6 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.5 30.9 - - + +
68A TYR* 4.4 3.9 - - + -
69A LEU* 4.1 10.8 - - + -
75A ILE* 3.8 25.3 - - + +
82A SER 3.3 12.2 + - - +
83A PHE 3.1 8.1 + - - +
85A ASP* 1.4 75.0 - - - +
87A PHE* 1.4 60.9 + - - +
89A PHE* 3.8 1.8 - - - +
90A SER* 3.0 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.4 52.5 - - + -
61A ASN* 3.6 25.8 - - + -
62A ALA* 3.7 10.5 - - + -
65A ALA* 3.6 8.2 - - + +
83A PHE* 2.7 35.8 + + + +
84A THR* 3.6 7.0 - - - +
86A ALA* 1.4 69.0 - - - +
88A PHE* 1.3 88.4 + + - +
90A SER* 3.2 5.5 + - - -
91A VAL* 2.8 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.0 49.0 + - + +
85A ASP* 4.2 3.8 - - - +
87A PHE* 1.3 96.7 - + - +
89A PHE* 1.3 64.6 + - - +
91A VAL* 3.3 12.1 + - + +
92A GLN* 3.0 40.7 + - - +
102A LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.5 38.1 - + - -
75A ILE* 3.8 28.9 - - + -
85A ASP 2.9 19.5 + - - +
86A ALA* 3.8 3.1 - - - +
88A PHE* 1.3 76.3 - - - +
90A SER* 1.4 54.6 + - - +
92A GLN* 3.1 10.6 + - + +
93A THR* 2.8 51.6 + - - -
102A LEU* 3.4 48.6 - - + +
103A ILE* 4.0 1.6 - - - -
104A PRO* 3.9 25.4 - - + -
113A VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 2.7 36.6 + - - +
64A PHE* 3.5 7.4 - - - +
65A ALA 4.3 0.7 - - - -
68A TYR* 4.2 4.7 - - - -
86A ALA 3.0 16.1 + - - -
87A PHE 3.2 9.4 + - - -
89A PHE* 1.4 75.8 - - - +
91A VAL* 1.4 52.6 + - - +
93A THR* 3.1 2.0 + - - -
94A MET 2.8 31.2 + - - -
116A GLU* 2.3 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.7 24.0 - - + +
58A LEU* 5.8 0.4 - - + -
61A ASN* 3.5 23.6 - - - +
87A PHE* 2.8 46.0 + - + +
88A PHE* 3.3 15.4 + - + +
90A SER* 1.4 71.1 - - - +
92A GLN* 1.4 56.7 + - + +
94A MET* 4.1 0.8 - - - +
95A ALA* 2.9 38.9 + - + +
97A ILE* 4.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.0 28.0 + - - +
89A PHE* 3.1 10.7 + - + +
91A VAL* 1.4 75.9 - - + +
93A THR* 1.3 57.4 + - - +
96A THR 3.6 1.4 + - - -
97A ILE* 2.9 38.6 + - + -
98A GLY* 3.0 18.4 + - - +
99A TYR* 3.4 47.8 + - + +
100A GLY 4.9 0.3 + - - -
101A LYS* 5.4 0.9 + - - +
102A LEU* 4.2 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.8 9.6 - - - +
89A PHE* 2.8 38.6 + - - -
90A SER* 3.5 3.8 - - - -
92A GLN* 1.3 75.8 - - - +
94A MET* 1.4 58.9 + - - +
95A ALA 3.4 0.2 - - - -
96A THR* 3.0 25.2 + - - +
113A VAL* 3.9 36.5 - - + +
116A GLU* 3.6 21.3 - - + +
117A ALA* 4.3 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.4 37.9 - - + +
60A THR* 4.1 24.2 - - - -
61A ASN* 3.6 23.8 - - - +
64A PHE* 5.3 0.4 - - + -
90A SER 2.8 19.8 + - - +
91A VAL 4.1 1.1 - - - +
93A THR* 1.4 73.5 - - - +
95A ALA* 1.3 58.6 + - - +
96A THR* 3.6 5.2 + - - +
116A GLU* 3.7 27.5 - - + +
117A ALA* 4.8 0.7 - - - +
119A CYS* 5.5 0.9 - - + -
120A GLY* 3.6 30.8 - - - +
121A MET* 4.4 0.3 + - - +
124A LEU* 3.8 22.3 - - + +
401A PEG 4.2 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.8 14.6 - - + +
91A VAL* 2.9 22.8 + - + +
94A MET* 1.3 72.8 - - - +
96A THR* 1.4 72.8 + - - +
97A ILE* 3.5 24.0 + - + +
124A LEU* 4.9 7.9 - - + -
----------------------------------------------------------
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