Contacts of the strand formed by residues 61 - 76 (chain C) in PDB entry 4LL4
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 GLN 61 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C MET* 3.5 4.5 - - - -
58C GLN* 2.7 41.7 + - + +
59C GLY 3.1 1.2 + - - -
60C SER* 1.3 82.5 + - - +
62C GLN* 1.3 69.4 + - - +
63C CYS* 4.9 3.4 - - - -
299C ARG* 4.0 52.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.0 50.5 - - + +
56C TRP 3.3 12.8 - - - +
57C MET* 3.9 19.3 - - + +
61C GLN* 1.3 79.6 + - - +
63C CYS* 1.3 66.9 + - - +
64C LYS* 5.4 2.0 - - + -
298C SER 3.5 8.5 - - - +
299C ARG* 3.5 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.5 1.2 - - - -
56C TRP* 2.8 58.4 + - + -
58C GLN* 4.1 11.0 - - - -
61C GLN* 4.3 8.1 - - - -
62C GLN* 1.3 80.3 - - - +
64C LYS* 1.3 60.5 + - - +
190C CYS* 2.1 51.6 - - + -
297C GLY 4.4 3.1 - - - -
298C SER 3.2 10.5 - - - +
299C ARG* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 4.1 25.1 - - + +
54C VAL 3.3 10.8 - - - +
55C LEU* 3.9 26.1 - - + +
62C GLN* 4.2 3.1 - - + -
63C CYS* 1.3 75.6 - - - +
65C GLN* 1.3 61.0 + - - +
66C THR* 3.6 23.5 + - - +
297C GLY* 3.2 5.1 - - - -
298C SER* 3.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA 3.9 0.5 - - - +
53C LYS* 3.5 3.3 - - - -
54C VAL* 2.8 45.3 + - + +
56C TRP* 4.6 1.8 - - - -
64C LYS* 1.3 74.7 - - - +
66C THR* 1.3 68.4 + - - +
67C SER* 4.3 11.7 + - - +
272C VAL* 3.0 29.9 + - - +
273C GLU* 5.0 0.4 - - - +
274C TYR* 3.8 16.0 - - - -
294C LEU 4.8 1.1 + - - +
295C VAL* 3.2 24.3 - - + +
296C ILE 3.1 36.1 + - - +
297C GLY* 3.8 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 4.1 15.9 - - + -
52C ALA 3.3 9.4 - - - +
53C LYS* 4.1 8.9 - - + +
64C LYS* 3.6 27.6 + - - +
65C GLN* 1.3 75.8 + - - +
67C SER* 1.3 67.9 + - - +
68C GLU* 5.0 4.0 - - + +
270C LEU 4.3 5.8 - - - +
271C ARG* 4.5 4.9 - - - -
272C VAL 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 3.2 6.6 - - - -
52C ALA* 2.7 44.4 + - - +
54C VAL* 6.0 1.7 - - - +
65C GLN* 4.3 16.5 + - - +
66C THR* 1.3 76.7 + - - +
68C GLU* 1.3 60.8 + - - +
69C TYR* 3.5 28.2 + - - -
271C ARG* 3.7 21.1 - - - +
272C VAL 4.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C CYS* 5.7 3.9 - - + +
50C GLY 3.4 9.9 - - - +
51C VAL* 4.4 10.8 - - + +
66C THR* 4.3 4.2 - - + +
67C SER* 1.3 70.9 - - - +
69C TYR* 1.3 60.6 + - - +
70C LEU 4.6 2.7 - - - +
71C ARG* 2.8 54.8 + - - +
269C ILE 4.9 2.4 - - - +
270C LEU* 2.9 38.4 + - + +
271C ARG* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLY 2.9 9.6 + - - +
51C VAL* 4.7 1.6 - - - -
52C ALA* 3.9 12.7 - - + +
67C SER* 3.5 32.3 + - - -
68C GLU* 1.3 70.6 - - - +
70C LEU* 1.3 53.3 + - - +
106C PRO* 2.8 36.6 - - + +
109C PRO* 2.9 28.9 - - + +
110C LEU* 3.6 11.7 - - + -
111C GLY* 3.6 29.0 - - - -
121C VAL* 5.2 0.2 - - + -
123C TYR* 3.4 25.1 - + + +
270C LEU* 4.5 6.3 - - - +
271C ARG* 3.3 37.6 + - - +
273C GLU* 4.7 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA* 3.1 32.3 - - + +
49C CYS* 3.1 31.3 - - - +
50C GLY* 3.1 13.4 + - - +
68C GLU* 3.6 3.7 - - - +
69C TYR* 1.3 80.5 - - - +
71C ARG* 1.3 59.8 + - - +
72C TYR* 3.7 21.1 - - + -
103C PHE* 4.2 16.2 - - + -
104C GLU 4.0 20.4 - - - +
105C LEU* 4.3 9.4 - - + -
106C PRO* 4.1 14.4 - - + -
123C TYR* 4.5 8.1 - - + -
143C PHE* 4.4 7.6 - - + -
270C LEU* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN* 3.8 31.6 + - - +
226A GLN* 4.4 3.3 - - - +
47C LEU* 4.6 13.5 - - + -
48C ALA 4.2 0.9 - - - -
49C CYS* 5.1 4.0 - - - -
68C GLU* 2.8 34.7 + - - +
70C LEU* 1.3 72.1 - - - +
72C TYR* 1.3 60.8 + - - +
73C GLU* 4.2 2.1 + - + +
222C LEU* 4.0 21.5 - - + +
267C SER 3.2 27.2 + - - -
268C ASN* 4.6 3.0 - - - +
269C ILE 4.7 2.8 + - - -
270C LEU* 3.3 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 4.4 31.2 - - + +
227A THR* 5.0 4.9 - - + -
228A LYS* 6.2 1.6 - - + -
46C ILE* 4.2 11.6 - - + +
47C LEU* 3.3 4.8 - - - +
48C ALA* 2.9 42.8 + - + +
70C LEU* 3.7 21.8 - - + -
71C ARG* 1.3 78.1 - - - +
73C GLU* 1.3 71.1 + - - +
74C ASP* 3.4 26.3 + - + +
101C PHE* 5.9 0.3 - - - +
102C GLY 2.7 22.3 + - - -
103C PHE* 3.1 40.8 - + + -
104C GLU 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN* 6.0 4.4 - - - +
226A GLN* 6.2 0.4 - - - +
228A LYS* 3.1 27.2 - - - +
45C ARG* 4.5 21.3 + - + -
46C ILE 3.4 11.7 - - - +
47C LEU* 4.3 25.1 - - + +
71C ARG* 4.2 1.7 + - + +
72C TYR* 1.3 80.9 - - - +
74C ASP* 1.3 79.3 + - - +
128C PHE* 4.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 4.0 23.2 + - - +
229A VAL 5.7 0.7 - - - +
45C ARG* 3.6 6.6 - - - +
46C ILE* 2.8 43.7 + - + +
72C TYR* 3.4 27.7 + - + -
73C GLU* 1.3 83.7 - - - +
75C THR* 1.4 91.9 + - - +
76C LEU* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 4.5 13.9 - - + -
44C VAL 3.5 14.8 - - - +
45C ARG* 4.0 18.6 - - + +
74C ASP* 1.4 93.2 + - - +
76C LEU* 1.3 72.1 + - - +
77C LEU* 3.9 4.2 + - - +
85C GLU* 4.2 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 3.6 31.6 - - + -
44C VAL* 2.8 29.9 + - + +
46C ILE* 3.9 33.4 - - + -
74C ASP* 4.4 9.4 - - - +
75C THR* 1.3 81.7 - - - +
77C LEU* 1.3 65.0 + - - +
81C GLN* 4.2 3.3 + - - +
85C GLU* 5.7 0.2 - - - +
99C TYR* 3.4 39.9 - - + +
100C LYS 3.6 17.3 - - - +
101C PHE* 4.0 15.7 - - + -
----------------------------------------------------------
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