Contacts of the helix formed by residues 82 - 94 (chain K) in PDB entry 5C3I
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 THR 82 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J GLN* 3.9 17.7 - - - +
88J ALA* 3.5 10.4 - - - +
78K ARG* 3.6 21.3 - - - +
80K THR 4.1 0.4 - - - +
81K VAL* 1.3 76.9 - - - +
83K ALA* 1.3 63.9 + - - +
84K MET 3.3 2.5 + - - -
85K ASP* 3.0 43.9 + - - +
86K VAL* 3.5 3.6 + - - +
102L VAL* 3.8 23.1 - - + +
103L GLU 4.6 0.9 - - - +
104L GLU* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ARG* 4.5 10.8 - - - +
85J GLN* 4.4 4.9 + - - -
87J SER* 3.8 31.4 - - - +
88J ALA* 3.7 13.0 - - - +
91J ALA* 4.6 5.8 - - + +
82K THR* 1.3 72.8 - - - +
84K MET* 1.3 57.0 + - + +
86K VAL* 3.3 6.2 + - - +
87K VAL* 2.8 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K THR* 3.1 1.4 + - - -
83K ALA* 1.3 80.9 - - + +
85K ASP* 1.3 58.7 + - - +
87K VAL* 3.6 28.4 - - + +
88K TYR* 2.8 57.3 + - + +
104L GLU* 3.3 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K ALA* 3.8 18.1 - - + +
72K TYR* 3.4 16.9 - - + -
73K THR* 2.9 22.6 + - - -
78K ARG* 2.9 29.0 + - - -
81K VAL* 4.0 6.1 - - + -
82K THR* 3.0 33.8 + - - +
84K MET* 1.3 77.4 - - - +
86K VAL* 1.3 57.1 + - - +
88K TYR* 4.7 1.6 - - - -
89K ALA* 3.1 26.5 + - - +
104L GLU* 4.7 0.5 - - - +
105L LEU* 3.2 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ALA* 3.8 16.2 - - + +
91J ALA* 4.3 5.8 - - + -
92J LEU* 3.8 52.3 - - + +
65K VAL* 4.3 2.0 - - + -
69K ALA* 4.1 17.0 - - + -
81K VAL* 4.5 4.5 - - + -
82K THR 3.5 11.4 + - - +
83K ALA 3.3 7.7 + - - +
84K MET 3.2 0.2 - - - -
85K ASP* 1.3 74.6 - - - +
87K VAL* 1.3 55.9 + - - +
89K ALA* 3.0 2.7 + - - +
90K LEU* 2.8 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ARG* 6.1 2.5 - - - +
91J ALA* 5.4 7.0 - - + -
83K ALA* 2.8 29.7 + - + +
84K MET* 3.6 31.6 - - + +
86K VAL* 1.3 72.9 - - - +
88K TYR* 1.3 64.8 + - + +
90K LEU* 3.4 12.3 + - + +
91K LYS* 3.2 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I HIS* 5.7 1.7 - - - -
72K TYR* 3.6 32.0 + + + +
84K MET* 2.8 41.3 + - + +
85K ASP* 3.8 3.8 - - - +
87K VAL* 1.3 79.1 - - + +
89K ALA* 1.3 62.5 + - - +
91K LYS* 3.4 38.1 + - + +
92K ARG* 3.5 8.5 + - - +
104L GLU* 5.4 4.8 - - + +
105L LEU* 4.8 32.3 + - + -
110L ARG* 4.2 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K VAL* 3.6 28.7 - - + +
68K ASP* 3.7 9.7 - - + +
69K ALA* 3.6 15.0 - - + +
72K TYR* 3.5 7.8 - - + -
85K ASP 3.1 17.4 + - - +
86K VAL 3.0 5.3 + - - +
88K TYR* 1.3 75.8 - - - +
90K LEU* 1.3 62.1 + - - +
92K ARG* 3.4 8.9 - - - +
93K GLN* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ALA* 4.4 4.7 - - + +
95J ALA* 3.5 35.7 - - + -
61K PHE* 4.3 8.5 - - + -
65K VAL* 4.0 27.8 - - + -
86K VAL* 2.8 30.2 + - + +
87K VAL* 3.7 11.7 - - + +
88K TYR 3.2 0.4 - - - -
89K ALA* 1.3 75.5 - - - +
91K LYS* 1.3 62.9 + - - +
92K ARG 3.2 2.5 - - - -
93K GLN* 3.6 6.1 + - + +
94K GLY 3.5 15.6 + - - -
95K ARG* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ARG 4.5 1.6 - - - +
149I PHE* 4.4 0.7 - - - -
150I HIS* 3.4 34.1 + - + +
87K VAL* 3.2 31.7 - - - +
88K TYR* 3.7 32.7 - - + +
89K ALA 3.4 0.4 - - - -
90K LEU* 1.3 77.4 - - + +
92K ARG* 1.3 61.7 + - - +
94K GLY* 3.7 8.0 + - - -
95K ARG* 3.9 40.6 + - - +
110L ARG* 4.6 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I PHE* 4.5 8.3 - - - +
150I HIS* 4.5 27.1 + - + +
68K ASP* 3.0 35.4 + - - +
72K TYR* 4.5 6.5 - - - +
88K TYR 3.5 9.2 + - - +
89K ALA* 3.4 12.1 - - - +
90K LEU 3.2 0.2 - - - -
91K LYS* 1.3 81.5 - - - +
93K GLN* 1.3 65.4 + - - +
94K GLY 3.5 0.3 + - - -
114L GLU* 4.2 8.0 + - + +
117L MET* 3.3 56.4 - - - +
118L ARG* 3.7 16.8 - - - +
120L ARG* 4.0 4.9 - - - +
121L ASP* 3.8 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I THR* 5.5 0.2 - - - +
149I PHE* 3.5 15.9 - - - -
61K PHE* 5.1 13.4 - - + -
64K ASN* 3.5 38.3 + - - +
65K VAL* 3.7 24.0 - - + -
68K ASP* 3.6 21.2 + - - -
89K ALA 3.3 15.1 + - - +
90K LEU* 3.6 7.6 + - + +
91K LYS 3.4 0.2 - - - -
92K ARG* 1.3 78.8 + - - +
94K GLY* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I THR* 4.1 8.0 - - - +
148I ARG 3.2 17.7 - - - -
149I PHE* 3.7 14.1 - - - -
61K PHE* 6.1 1.2 - - - -
90K LEU 3.5 5.7 + - - +
91K LYS 3.7 4.2 + - - -
92K ARG 3.3 3.2 - - - -
93K GLN* 1.3 84.1 - - - +
95K ARG* 1.3 64.8 + - - +
96K THR* 4.3 0.9 + - - -
----------------------------------------------------------
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