Contacts of the strand formed by residues 72 - 80 (chain I) in PDB entry 6AHU
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 72 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A C 3.4 47.6 + - - +
31I SER 3.2 6.4 + - - +
32I VAL* 3.5 45.0 - - + +
33I VAL 3.7 0.5 + - - -
70I PRO 3.7 5.1 + - - +
71I ILE* 1.3 68.7 - - - +
73I ILE* 1.3 61.4 + - - +
74I LEU* 3.7 9.5 + - + +
229I LEU* 5.4 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL* 4.9 17.9 - - + -
33I VAL* 3.4 17.5 - - + +
35I ILE* 5.2 7.0 - - + -
54I VAL* 3.8 42.8 - - + -
58I PHE* 5.1 13.2 - - + -
62I PRO* 5.2 6.1 - - + -
71I ILE* 3.2 29.2 + - + +
72I LYS* 1.3 70.2 - - - +
74I LEU* 1.3 71.5 - - - +
75I THR* 5.4 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I VAL* 4.0 15.7 - - + -
33I VAL 3.5 5.1 + - - -
34I ALA* 3.4 28.8 - - + -
35I ILE* 3.5 6.1 + - - +
72I LYS* 3.7 15.4 + - + +
73I ILE* 1.3 85.8 - - - +
75I THR* 1.3 69.8 + - - +
76I ARG* 4.0 26.7 - - + +
101I ASP* 4.9 11.4 - - + +
102I VAL* 5.3 2.2 - - + -
229I LEU* 3.8 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I ILE* 4.2 6.1 - - + +
37I HIS* 5.5 4.7 - - - +
51I PRO* 5.4 7.4 - - + -
52I VAL* 6.3 1.6 - - + -
54I VAL* 5.3 12.6 - - + -
73I ILE* 5.4 1.6 - - + +
74I LEU* 1.3 80.4 - - - +
76I ARG* 1.3 64.0 + - - +
100I TYR* 3.6 44.1 + - + -
101I ASP* 3.7 11.5 + - - +
102I VAL 4.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ASP* 5.7 3.4 + - - +
8I ASP* 2.4 50.3 + - - -
32I VAL* 5.1 5.9 - - - +
34I ALA* 4.0 11.6 - - + +
35I ILE 3.0 20.3 + - - +
36I ASN* 3.3 25.1 - - - +
37I HIS* 3.6 10.4 + - - -
74I LEU* 4.0 24.0 - - + +
75I THR* 1.3 78.8 - - - +
77I LEU* 1.3 62.4 + - - +
100I TYR* 4.9 2.5 - - - -
102I VAL* 3.5 47.9 - - + +
104I ALA* 6.2 2.0 - - + -
124I LEU* 4.6 9.1 - - - +
225I CYS 4.8 4.6 + - - -
228I ALA* 3.9 25.4 - - - +
229I LEU* 4.6 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ASN* 4.7 0.6 - - - +
37I HIS* 3.7 24.7 - - + +
39I VAL* 3.8 22.0 - - + -
48I ILE* 5.7 4.3 - - + -
76I ARG* 1.3 75.6 - - - +
78I THR* 1.3 67.5 + - - +
79I ILE* 3.7 29.8 - - + -
100I TYR* 3.6 43.2 - - + +
102I VAL 3.5 6.1 + - - +
103I VAL* 5.1 6.1 - - + -
104I ALA* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ARG* 4.0 19.9 + - - +
36I ASN* 3.5 27.6 + - - +
37I HIS 2.9 30.3 + - - +
38I ILE* 3.9 6.5 - - + -
39I VAL* 3.2 14.6 + - - +
77I LEU* 1.3 74.6 + - - +
79I ILE* 1.3 67.7 + - - +
80I ILE* 3.9 10.5 + - + +
104I ALA* 3.4 5.8 - - - +
106I PHE* 5.1 1.3 - - + -
126I CYS* 3.7 28.1 - - + -
153I GLU* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I VAL* 3.5 15.0 - - + +
77I LEU* 3.7 32.8 - - + +
78I THR* 1.3 72.7 - - - +
80I ILE* 1.3 60.2 + - - +
81I VAL* 3.5 12.7 + - + -
86I HIS* 3.6 29.2 - - + -
90I LEU* 3.8 25.1 - - + -
103I VAL* 3.8 20.9 - - + -
104I ALA 3.1 21.0 + - - +
105I VAL* 3.6 7.0 - - + +
106I PHE* 2.7 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ILE* 3.9 27.4 - - + -
39I VAL 2.8 19.2 + - - +
40I ASP* 3.9 24.7 - - + +
41I PHE* 4.3 10.5 + - + -
78I THR* 4.9 10.3 - - + +
79I ILE* 1.3 71.0 - - - +
81I VAL* 1.3 64.2 + - - +
82I SER 4.2 1.0 + - - -
86I HIS* 3.9 8.3 + - - -
106I PHE* 3.7 31.0 - - + -
108I LYS* 4.1 19.1 - - - +
----------------------------------------------------------
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