Contacts of the helix formed by residues 67 - 83 (chain K) in PDB entry 1VCB
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 67 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J PHE* 3.6 18.8 - - - -
94J SER* 3.3 16.3 + - - -
23K SER* 3.4 6.9 + - - -
25K ASP* 2.4 38.2 + - - -
27K HIS* 2.7 19.6 + - - -
29K PHE* 4.1 6.3 - - - -
66K PRO* 1.3 72.7 - - - +
68K HIS* 1.3 58.6 + - - +
69K VAL 3.0 0.2 - - - -
70K LEU 4.6 0.2 - - - +
71K SER* 3.0 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J PHE* 4.0 7.8 - - + +
94J SER* 2.7 40.8 + - - +
95J SER 4.1 5.8 - - - -
96J PRO* 3.5 37.6 - - + +
97J PRO* 5.1 0.4 - - + -
66K PRO* 3.4 29.0 - - + +
67K SER* 1.3 78.3 - - - +
69K VAL* 1.3 61.9 + - + +
71K SER* 3.6 12.6 + - - -
72K LYS* 4.3 4.9 - - - +
99K ILE* 3.8 34.4 - - + +
102K GLU* 3.1 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K ILE* 3.4 21.8 - - + -
66K PRO* 3.1 20.8 + - + +
67K SER 3.0 0.8 - - - -
68K HIS* 1.3 89.8 - - + +
70K LEU* 1.3 60.4 + - - +
71K SER 3.1 1.3 - - - -
72K LYS* 2.8 25.5 + - - +
73K VAL* 3.1 10.4 + - + +
99K ILE* 5.0 6.3 - - + +
102K GLU* 3.5 32.1 - - + +
103K LEU* 4.0 15.9 - - + +
106K ALA* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 4.0 16.8 - - + +
22K ILE 3.9 6.1 - - - -
23K SER* 3.8 29.4 - - - +
29K PHE* 3.8 25.4 - - + -
62K PHE* 4.0 19.3 - - + -
65K ILE* 3.7 17.0 - - + +
66K PRO 2.9 19.1 + - - +
69K VAL* 1.3 73.6 - - - +
71K SER* 1.3 60.8 + - - +
73K VAL* 4.0 23.1 - - + -
74K CYS* 3.1 35.8 + - - -
110K LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 3.7 9.6 - - - -
93J PHE* 3.7 33.3 - - - -
29K PHE* 4.1 11.1 - - - -
67K SER 3.0 19.2 + - - -
68K HIS* 3.6 11.6 + - - -
70K LEU* 1.3 77.4 - - - +
72K LYS* 1.3 59.6 + - - +
74K CYS 3.4 0.2 + - - -
75K MET* 3.0 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J GLN 3.9 12.1 + - - -
68K HIS 4.3 11.4 - - - +
69K VAL 2.8 10.7 + - - +
71K SER* 1.3 81.9 + - - +
73K VAL* 1.3 65.5 + - - +
75K MET* 3.1 18.3 + - + +
76K TYR* 2.8 23.2 + - - +
93K PHE* 3.8 20.6 - - + -
94K PRO* 2.9 42.0 + - - +
95K ILE* 4.8 6.0 - - - +
96K ALA* 5.2 2.5 - - - +
99K ILE* 4.4 24.0 - - + -
103K LEU* 4.2 20.2 - - + -
158L LEU* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ILE* 5.6 0.4 - - + -
65K ILE* 5.3 0.7 - - + -
69K VAL* 3.1 18.9 + - + +
70K LEU* 3.6 24.5 - - + +
72K LYS* 1.3 75.1 - - - +
74K CYS* 1.3 64.9 + - - +
76K TYR* 3.0 10.0 + - - +
77K PHE* 3.0 52.1 + - + -
103K LEU* 3.9 18.4 - - + -
106K ALA* 4.5 3.1 - - + -
110K LEU* 3.6 27.6 - - + -
112K CYS* 5.2 0.2 - - - -
158L LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 3.5 31.0 - - + -
21K LEU* 3.8 20.6 - - - -
29K PHE* 4.0 15.9 - - - -
31K VAL* 3.6 26.5 - - + +
70K LEU* 3.1 21.3 + - - +
72K LYS 3.2 0.2 - - - -
73K VAL* 1.3 77.7 - - - +
75K MET* 1.3 63.6 + - - +
77K PHE* 3.0 22.4 + - - +
78K THR* 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J MET* 4.0 29.4 - - + -
15J PHE* 3.8 13.7 - - + -
69J PRO 3.4 13.5 - - - +
70J GLN 3.6 23.3 - - - +
71J ALA* 4.6 2.0 - - - -
72J PRO* 3.8 15.5 - - + -
93J PHE* 5.7 1.3 - - + -
71K SER* 3.0 33.7 + - - +
72K LYS* 3.1 25.8 + - + +
74K CYS* 1.3 76.9 - - - +
76K TYR* 1.4 56.7 + - - +
78K THR* 3.2 8.2 + - - -
79K TYR* 3.1 26.2 + - - +
93K PHE* 4.1 6.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K THR* 4.3 8.7 - - + -
72K LYS 2.8 12.3 + - - +
73K VAL* 3.0 12.1 + - - +
75K MET* 1.4 73.8 - - - +
77K PHE* 1.3 75.0 - + - +
79K TYR* 3.3 21.8 - + - +
80K LYS* 2.8 52.8 + - + +
93K PHE* 3.6 23.8 - + + -
112K CYS* 3.6 16.1 + - + -
155L VAL* 4.1 2.3 - - - +
156L TYR 2.7 29.6 + - - -
157L THR* 3.2 10.2 - - - -
158L LEU* 3.4 39.3 - - + -
161L ARG* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 4.4 8.3 - - + -
31K VAL* 4.7 8.1 - - + -
35K HIS* 3.4 29.6 - - + +
36K ALA* 3.7 21.5 - - + -
38K THR* 3.9 20.9 - - + -
39K SER* 4.0 19.7 - - - -
42K ILE* 4.2 13.9 - - + -
73K VAL* 3.0 44.7 + - + -
74K CYS* 3.0 14.6 + - - +
76K TYR* 1.3 83.0 - + - +
78K THR* 1.3 62.5 + - + +
80K LYS* 3.9 2.8 - - - +
81K VAL* 3.0 29.5 + - - +
110K LEU* 4.9 0.4 - - + -
112K CYS* 4.1 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 4.7 15.7 - - + +
15J PHE* 4.6 25.6 - - + -
16J THR* 5.9 1.6 - - - +
69J PRO* 3.2 24.6 + - - +
72J PRO* 5.9 0.3 - - - +
31K VAL* 5.5 1.8 - - + -
35K HIS* 3.6 28.0 + - + -
74K CYS 3.3 13.3 + - - +
75K MET* 3.2 12.5 + - - -
77K PHE* 1.3 76.4 - - + +
79K TYR* 1.3 56.2 + - - +
81K VAL* 3.4 1.7 + - - +
82K ARG* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J PRO* 3.8 12.1 - - + -
70J GLN* 3.5 27.6 - - + +
75K MET 3.1 14.5 + - - +
76K TYR* 3.3 24.2 - + - +
78K THR* 1.3 78.2 + - - +
80K LYS* 1.3 66.8 + - - +
82K ARG* 3.2 1.1 + - - -
83K TYR* 3.0 53.5 + + - +
90K ILE* 3.5 13.6 - - + +
91K PRO* 2.7 28.6 + - + -
92K GLU* 4.4 0.2 - - - -
93K PHE* 3.7 34.6 + + + +
153L LEU* 5.2 1.7 - - - +
154L PRO 4.7 4.3 + - - -
155L VAL* 4.1 18.8 - - + -
156L TYR 5.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K THR* 3.8 32.1 + - + +
76K TYR* 2.8 46.8 + - + +
77K PHE 3.9 2.9 - - - +
79K TYR* 1.3 72.0 - - - +
81K VAL* 1.3 70.2 + - - +
84K THR* 3.0 55.3 + - + +
155L VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K GLU* 4.8 4.7 - - + +
35K HIS* 3.7 41.7 - - + +
38K THR* 3.7 19.3 - - - +
77K PHE 3.0 18.4 + - - +
78K THR 4.0 3.1 - - - +
80K LYS* 1.3 83.8 - - + +
82K ARG* 1.3 61.8 + - - +
84K THR* 4.6 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J MET* 5.8 8.7 - - - +
2J ASP* 5.5 5.7 + - - +
4J PHE* 4.1 23.8 - - + -
69J PRO* 4.1 18.1 - - + +
78K THR 2.9 19.4 + - - +
79K TYR 3.7 3.6 - - - +
80K LYS 3.1 0.2 - - - -
81K VAL* 1.3 80.8 - - - +
83K TYR* 1.3 91.6 + - + +
84K THR 4.6 1.6 - - - +
86K SER* 4.1 8.7 + - - -
88K THR* 4.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J ARG* 5.5 1.6 + - - -
69J PRO* 4.3 9.6 - - + +
70J GLN* 4.1 11.3 + - - -
79K TYR* 3.0 47.1 + + + +
82K ARG* 1.3 118.0 + - + +
84K THR* 1.3 69.8 + - - +
85K ASN 3.3 1.2 + - - -
86K SER* 3.1 17.8 + - - -
88K THR* 4.4 10.8 - - - -
89K GLU 4.4 4.3 - - - -
90K ILE* 3.8 35.4 - - + +
91K PRO* 3.5 37.1 - - + +
155L VAL* 3.8 7.8 - - + +
----------------------------------------------------------
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