Contacts of the strand formed by residues 59 - 67 (chain M) in PDB entry 1TH7
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 GLY 59 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M GLU* 3.4 29.0 + - - +
52M GLU 3.5 5.6 - - - -
53M ILE* 4.4 2.2 - - - -
54M GLN* 4.9 1.3 - - - -
57M GLY 4.0 0.2 + - - -
58M SER* 1.3 80.0 + - - +
60M LYS* 1.3 60.1 + - - -
61M LYS* 4.0 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LYS* 6.3 0.6 - - - +
31L GLU* 4.7 13.5 + - - -
51M GLU* 3.1 2.3 - - - -
52M GLU* 2.8 59.8 + - + +
54M GLN* 3.7 17.7 - - + +
59M GLY* 1.3 72.3 - - - -
61M LYS* 1.3 71.5 + - - +
62M LEU* 3.4 13.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M SER 3.6 8.5 - - - +
51M GLU* 4.3 5.8 - - + +
59M GLY 4.0 3.7 + - - +
60M LYS* 1.3 78.4 - - - +
62M LEU* 1.3 66.9 + - - +
63M GLY* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LEU* 5.8 4.5 - - + -
25L LYS* 3.5 35.7 - - - +
74L LEU* 4.6 7.4 - - + -
76L SER* 3.0 28.7 + - - +
77L PRO 4.9 2.8 - - - +
32M VAL* 4.7 2.0 - - + -
50M SER* 2.8 18.6 + - - +
51M GLU 4.4 2.5 - - - -
52M GLU* 3.7 20.2 - - + +
60M LYS* 3.7 22.4 - - - +
61M LYS* 1.3 81.7 - - - +
63M GLY* 1.3 62.0 + - - +
64M THR 3.5 0.5 + - - -
65M ILE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M SER 3.5 0.7 - - - -
49M ASP* 3.2 15.7 + - - -
50M SER* 2.7 42.9 + - - -
61M LYS* 3.8 4.1 - - - +
62M LEU* 1.3 77.6 - - - +
64M THR* 1.3 57.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L VAL* 4.1 35.4 - - + -
76L SER* 3.0 19.9 + - - -
77L PRO* 3.2 19.1 + - + +
46M VAL* 4.2 9.0 - - + -
47M LEU 3.3 11.0 - - - +
48M SER* 3.9 15.0 - - - +
49M ASP 4.7 0.5 + - - -
62M LEU 3.5 1.4 + - - -
63M GLY* 1.3 72.8 - - - -
65M ILE* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L LEU* 4.2 18.4 - - + -
75L ILE 3.4 5.6 - - - +
76L SER* 3.7 19.5 - - - +
77L PRO* 5.1 0.2 - - - -
32M VAL* 4.3 13.2 - - + -
45M LEU 3.8 0.3 - - - +
46M VAL* 3.2 7.4 - - - +
47M LEU* 2.9 48.0 + - + +
50M SER* 3.4 30.3 - - - +
62M LEU* 3.9 19.1 - - + -
64M THR* 1.3 81.0 - - - +
66M VAL* 1.3 64.9 + - - +
67M ILE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L MET* 4.5 15.0 - - + -
10L ALA* 4.6 2.0 - - + +
13L VAL* 3.6 35.9 - - + -
14L LEU* 4.3 17.5 - - + -
43L MET* 3.8 28.1 - - + +
74L LEU* 3.1 5.6 - - - -
75L ILE* 2.9 40.9 + - + +
44M ASN* 6.1 0.9 - - + -
45M LEU 3.3 8.7 - - - +
46M VAL* 4.2 10.5 - - + -
65M ILE* 1.3 73.2 - - - +
67M ILE* 1.3 62.2 + - - +
68M ARG 4.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L MET* 4.2 3.8 - - - +
73L ILE 3.7 9.6 - - - +
74L LEU* 4.4 7.9 - - + -
24M VAL* 4.7 3.6 - - + -
26M LEU* 3.9 24.5 - - + -
32M VAL* 3.8 29.2 - - + -
44M ASN* 3.3 3.5 - - - +
45M LEU* 2.7 54.6 + - + +
47M LEU* 4.0 16.4 - - + -
65M ILE* 3.9 22.2 - - + +
66M VAL* 1.3 75.0 - - - +
68M ARG* 1.3 73.3 + - - +
69M GLY 3.3 0.9 + - - -
71M ASN* 5.1 0.9 - - + -
72M VAL* 4.0 9.9 - - + -
----------------------------------------------------------
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