Contacts of the strand formed by residues 49 - 57 (chain D) in PDB entry 1P7L
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 MET 49 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 5.6 1.1 - - + +
90A ALA* 4.1 7.4 - - + -
92A LEU* 3.6 34.3 - - + -
51C LEU* 4.0 25.1 - - + -
94C ALA* 4.0 22.9 - - + -
44D TYR* 4.0 17.0 - - + +
45D VAL* 3.4 0.3 - - - +
46D LYS* 2.9 36.2 + - + +
47D THR* 5.9 0.4 - - - -
48D GLY* 1.3 82.2 - - - +
50D VAL* 1.3 77.9 + - - +
51D LEU* 4.8 6.7 - - + +
84D PHE* 3.2 5.2 - - - -
90D ALA* 3.3 20.0 - - + +
92D LEU* 4.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 3.6 20.0 - - + -
43D THR* 4.0 13.2 - - + -
44D TYR 3.5 5.4 - - - +
45D VAL* 3.7 10.8 - - + -
49D MET* 1.3 84.5 - - - +
51D LEU* 1.3 58.0 + - - +
52D VAL* 4.1 6.3 - - + -
68D THR* 3.5 31.0 - - + -
72D VAL* 4.8 2.5 - - + -
84D PHE* 3.4 22.9 - - + -
89D CYS* 4.5 3.8 - - - -
90D ALA 2.9 10.8 + - - +
91D VAL* 3.5 2.2 - - + +
92D LEU* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.8 4.7 - - + -
44C TYR* 3.8 28.1 + - + -
49C MET* 3.9 11.9 - - + -
51C LEU* 3.5 29.2 - - + -
42D GLU 3.6 1.7 - - - +
43D THR* 3.0 7.3 - - - +
44D TYR* 2.6 51.3 + - + +
49D MET* 4.8 6.7 - - + +
50D VAL* 1.3 71.8 - - - +
52D VAL* 1.3 73.8 + - - +
53D GLY 3.9 0.9 - - - +
92D LEU* 3.6 27.4 - - + +
93D SER 4.1 3.8 - - - +
94D ALA* 4.3 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 4.2 8.5 - - + -
26D VAL* 4.3 11.2 - - + -
41D CYS* 3.5 29.6 - - - -
42D GLU 3.9 1.6 - - - -
43D THR* 4.1 5.8 - - + +
50D VAL* 4.1 15.5 - - + +
51D LEU* 1.3 75.0 - - - +
53D GLY* 1.3 57.7 + - - +
64D ILE* 3.7 32.1 - - + -
68D THR* 3.9 12.1 - - + +
91D VAL* 4.9 2.0 - - + -
92D LEU 2.8 12.7 + - - +
93D SER* 3.1 6.1 - - - -
94D ALA 3.0 20.1 + - - -
95D ILE* 3.5 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 3.2 16.5 + - - -
41D CYS* 3.4 10.0 - - - +
42D GLU 2.8 32.8 + - - -
52D VAL* 1.3 75.0 - - - +
54D GLY* 1.3 59.2 + - - -
56D ILE* 5.8 0.2 - - - +
94D ALA* 3.2 20.0 - - - -
95D ILE* 3.8 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 4.0 2.8 + - - -
46C LYS* 3.6 13.8 + - - +
239C CYS* 4.2 11.7 - - - -
40D ALA 3.4 7.2 - - - -
42D GLU 4.4 1.1 - - - -
53D GLY* 1.3 75.0 - - - -
55D GLU* 1.3 73.7 + - - +
56D ILE 4.2 0.2 - - - -
94D ALA 3.1 7.3 + - - +
95D ILE* 3.4 3.5 - - - -
96D GLY 2.8 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 2.6 41.7 + - - +
236C MET 4.4 0.6 - - - +
237C GLY 4.0 11.7 - - - +
238C ASP* 3.3 2.6 - - - +
239C CYS* 3.3 21.8 + - - +
685C SAM 3.0 44.0 + - - +
686C K 4.1 2.6 - - - -
38D ARG 4.0 2.1 - - - +
40D ALA* 2.9 36.6 + - + +
54D GLY* 1.3 72.9 - - - +
56D ILE* 1.3 62.6 + - - +
96D GLY 3.1 5.4 - - - +
97D LYS 3.6 24.9 - - - +
98D GLN* 3.8 5.1 - - - +
99D SER 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D VAL* 4.1 12.1 - - + -
30D ILE* 3.6 25.6 - - + -
38D ARG 3.5 6.5 - - - +
39D VAL* 4.0 22.9 - - + -
40D ALA 4.3 0.9 - - - +
41D CYS* 4.3 11.2 - - + -
53D GLY 5.9 0.2 - - - +
55D GLU* 1.3 79.4 - - - +
57D THR* 1.3 64.9 + - - +
58D THR* 3.6 27.5 + - + -
64D ILE* 5.8 1.1 - - + -
95D ILE* 3.7 30.3 - - + +
96D GLY 2.6 17.8 + - - +
97D LYS* 3.3 15.1 - - - +
98D GLN 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA* 4.1 1.6 - - - -
38D ARG* 2.9 37.8 + - + +
56D ILE* 1.3 70.7 - - - +
58D THR* 1.3 61.7 + - - +
97D LYS* 3.4 16.5 - - + +
98D GLN* 2.8 43.1 + - - +
103D ASN* 6.3 1.1 - - - +
----------------------------------------------------------
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