Contacts of the strand formed by residues 62 - 70 (chain G) in PDB entry 5HHM
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 PHE 62 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR* 3.6 37.5 - - + -
94F THR* 4.1 4.3 - - + -
96F GLN* 3.2 27.8 - - - -
29G GLY 2.9 23.8 + - - -
30G PHE* 3.2 48.3 + - + +
31G HIS* 3.4 27.1 - + - -
32G PRO 4.3 0.2 - - - -
33G SER* 3.9 31.0 - - - -
54G LEU* 3.8 17.0 - - + -
55G SER 3.4 17.7 - - - +
56G PHE* 3.8 4.0 - + + -
61G SER* 1.3 71.9 - - - +
63G TYR* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PHE* 5.4 2.3 - - - -
27F TYR* 3.4 22.4 + + - -
26G TYR* 3.8 28.3 - + + +
27G VAL 3.2 5.4 - - - +
28G SER* 3.6 20.9 - - - -
29G GLY 4.9 0.2 - - - +
30G PHE* 4.1 1.6 - - - -
52G SER* 4.9 3.1 + - - -
53G ASP 4.8 1.7 - - - +
54G LEU* 4.5 0.9 - - - +
55G SER* 3.2 40.4 + - - +
56G PHE* 3.6 26.6 + - - -
57G SER* 3.6 24.0 - - - +
62G PHE* 1.3 75.3 - - - +
64G LEU* 1.3 73.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G CYS 3.8 0.5 - - - +
26G TYR* 3.3 9.6 - - - -
27G VAL* 2.7 38.1 + - + +
30G PHE* 4.3 2.9 - - + -
33G SER 5.3 0.2 - - - +
35G ILE* 3.6 30.5 - - + -
51G HIS* 4.2 10.3 - - + -
52G SER* 3.0 37.9 - - - +
53G ASP 4.1 0.2 - - - -
54G LEU* 3.9 33.2 - - + +
63G TYR* 1.3 81.8 - - - +
65G LEU* 1.3 59.0 - - - +
66G TYR* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F PRO* 3.9 27.6 - - + +
236F ALA 4.6 1.6 - - - +
237F GLY* 4.0 25.6 - - - -
10G TYR* 3.4 24.7 - - - +
24G ASN* 3.8 20.9 - - + +
25G CYS 3.7 2.2 - - - +
26G TYR* 4.0 12.3 - - + -
50G GLU 3.9 0.2 - - - +
51G HIS* 3.2 6.6 - - - +
52G SER* 2.9 39.4 + - - +
64G LEU* 1.3 73.8 - - - +
66G TYR* 1.3 64.2 + - - +
67G TYR* 3.9 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU 3.9 0.5 - - - +
24G ASN* 3.4 3.1 - - - -
25G CYS* 2.7 44.7 + - + +
27G VAL* 4.3 3.8 - - + -
35G ILE* 3.8 22.9 + - + +
37G VAL* 3.5 56.3 + - + +
39G LEU* 4.1 5.0 - - + +
49G VAL* 3.8 22.9 - - + -
50G GLU 3.3 3.8 - - - +
51G HIS* 3.7 33.7 + + + -
64G LEU* 3.8 30.9 - - + +
65G LEU* 1.3 77.7 - - - +
67G TYR* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ARG* 5.6 4.2 + - - -
237F GLY* 6.0 2.9 - - - -
12G ARG* 4.8 9.4 - - - +
22G PHE* 4.4 21.5 - + + -
23G LEU 3.3 5.4 - - - -
24G ASN* 3.4 22.2 - - - +
39G LEU* 4.1 3.5 - - - +
48G LYS 4.3 0.3 - - - +
50G GLU* 2.8 84.4 + - + +
51G HIS* 4.0 14.5 + - - -
52G SER* 4.3 4.0 - - - -
65G LEU* 3.9 24.7 - - + -
66G TYR* 1.3 73.2 - - - +
68G THR* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G PHE* 3.3 9.6 - - - -
23G LEU* 2.8 45.5 + - + -
39G LEU* 3.7 20.9 - - + -
46G ILE* 3.5 36.8 - - + +
48G LYS* 2.6 25.9 + - - +
49G VAL* 4.3 2.2 - - - -
67G TYR* 1.3 74.9 - - - +
69G GLU* 1.3 67.1 + - - +
70G PHE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER* 4.7 15.8 + - - -
21G ASN 3.3 7.4 - - - +
22G PHE* 3.4 36.7 - - + -
46G ILE* 5.1 3.1 - - - +
48G LYS 5.0 0.4 + - - -
68G THR* 1.3 83.4 + - - +
70G PHE* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G SER* 4.3 6.1 - - - -
20G SER* 3.4 2.6 - - - -
21G ASN* 2.6 59.3 + - + +
22G PHE 3.6 8.5 - - - -
23G LEU* 3.4 44.6 - - + -
46G ILE* 5.8 1.1 - - + -
68G THR* 5.0 3.8 - - + -
69G GLU* 1.3 75.6 - - - +
71G THR* 1.3 59.9 + - - +
72G PRO* 3.6 13.1 - - + +
78G TYR* 3.5 40.4 - + + +
95G TRP* 3.4 46.7 - + - -
----------------------------------------------------------
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