Contacts of the strand formed by residues 61 - 69 (chain C) in PDB entry 2HHL
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 61 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE 5.6 0.2 + - - -
48A SER 4.1 10.4 + - - -
50A ALA* 2.8 26.0 + - + +
51A ASP 3.6 0.2 - - - -
52A PHE* 3.6 7.6 - - - +
53A ILE* 3.5 47.4 - - + +
57C GLU* 4.2 0.2 - - - -
58C ILE 2.8 37.0 + - - -
59C ASP* 3.9 5.9 + - - +
60C GLY* 1.3 77.6 - - - +
62C ILE* 1.3 60.5 + - - +
63C HIS* 3.3 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP 2.9 16.8 + - - +
52A PHE* 3.3 24.1 - - + +
53A ILE 3.1 24.6 + - - +
103A LEU* 3.7 20.5 - - + +
106A ARG* 5.7 10.3 - - - +
55C PRO* 3.7 31.0 - - + -
56C VAL 3.5 5.4 - - - +
57C GLU* 4.2 27.1 - - + +
60C GLY 4.9 1.8 - - - +
61C THR* 1.3 73.4 - - - +
63C HIS* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 43.5 + - + +
44C PHE* 3.5 47.3 - + + -
55C PRO* 3.5 0.5 - - - +
56C VAL* 2.7 43.9 + - - +
58C ILE* 4.1 19.5 - - + +
61C THR* 3.3 31.1 + - + +
62C ILE* 1.3 79.3 - - - +
64C GLN* 1.3 61.3 + - - +
65C VAL* 3.6 0.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE 4.8 2.2 + - - -
54A VAL* 6.2 0.4 - - + -
55A PRO* 6.4 2.0 - - + -
99A PRO* 5.2 4.3 - - + +
102A ASP* 3.9 26.3 + - - +
103A LEU* 3.3 39.5 - - + +
44C PHE* 3.4 27.4 - - - +
53C ILE* 3.5 26.2 - - + +
54C VAL 3.8 0.2 - - - -
55C PRO* 3.6 20.1 - - - +
62C ILE 4.3 0.2 - - - -
63C HIS* 1.3 71.7 - - - +
65C VAL* 1.3 60.2 + - - +
66C TYR* 3.8 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 3.6 29.6 - - - +
43C SER 3.7 7.6 - - - +
44C PHE* 3.7 26.5 - - + -
52C PHE 3.9 0.3 - - - +
53C ILE* 3.3 6.2 - - - -
54C VAL* 2.8 41.9 + - + +
56C VAL* 3.5 30.1 - - + -
63C HIS 4.3 0.2 - - - +
64C GLN* 1.3 70.4 - - - +
66C TYR* 1.3 62.2 + - - +
67C VAL* 3.9 4.8 + - + +
96C TYR* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 5.9 2.1 - - + +
99A PRO* 4.9 12.0 - - - +
102A ASP* 5.7 0.7 + - - -
42C SER* 3.0 5.4 - - - -
43C SER 2.9 41.8 + - - +
44C PHE 3.5 16.8 - - - -
45C LYS 3.6 11.2 - - - +
46C PRO* 3.6 28.5 - - + +
47C ILE* 3.6 46.0 - - + +
50C ALA* 4.2 2.5 - - + -
52C PHE 3.8 3.8 - - - -
53C ILE* 4.0 30.7 - - + -
64C GLN* 3.8 30.7 + - + +
65C VAL* 1.3 73.0 - - - +
67C VAL* 1.3 60.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.7 29.6 - - + -
41C HIS 3.7 2.0 - - - -
42C SER* 3.2 23.3 - - - +
47C ILE* 4.2 2.9 - - - -
50C ALA* 4.2 1.0 - - - +
51C ASP* 2.9 26.4 + - - +
52C PHE* 3.0 45.8 + - + +
54C VAL* 4.5 3.6 - - + -
65C VAL* 4.1 12.8 - - + +
66C TYR* 1.3 74.0 - - - +
68C LEU* 1.3 62.9 + - - +
100C VAL* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.2 5.7 - - - +
41C HIS 2.8 38.7 + - - +
47C ILE* 3.9 20.5 - - + +
49C ASN* 3.7 41.3 - - - +
50C ALA* 3.8 11.0 - - - -
51C ASP* 3.6 9.4 - - - +
67C VAL* 1.3 74.6 - - - +
69C LYS* 1.3 62.3 + - - +
163C TRP* 3.5 10.6 - - + -
164C PHE 4.3 10.5 - - - +
165C ASP* 4.4 9.0 - - + -
167C MET* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU 4.0 4.3 - - - -
40C VAL* 4.2 2.2 - - + -
51C ASP* 2.7 39.6 + - + +
52C PHE* 3.7 33.9 - - + -
68C LEU* 1.3 70.1 - - - +
70C ARG* 1.3 66.2 + - - +
71C PRO* 3.5 2.1 - - - +
73C VAL* 3.5 29.2 - - + -
74C ASP* 3.0 29.8 + - - -
104C LEU* 4.3 7.6 - - + -
106C ARG* 3.9 7.9 - - - +
163C TRP* 3.3 11.6 - - - -
167C MET* 4.5 7.3 - - - +
----------------------------------------------------------
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