Contacts of the strand formed by residues 38 - 46 (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 ARG 38 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C SAM 6.1 0.2 - - - -
36D LYS* 3.0 34.5 + - - +
37D ALA* 1.3 77.0 + - - +
39D VAL* 1.3 61.1 + - - +
40D ALA 4.1 0.2 - - - -
55D GLU 4.0 1.6 - - - +
56D ILE* 3.5 3.5 - - - -
57D THR* 2.9 48.2 + - + +
98D GLN* 4.0 35.5 - - + +
103D ASN* 4.4 2.4 - - - +
106D VAL* 3.6 10.7 - - + +
107D ASP* 2.4 43.4 + - - +
266D ASP* 3.2 9.1 + - - +
268D SER* 3.5 20.2 + - - +
269D LYS* 4.4 2.7 - - - +
338D TYR* 3.0 26.9 + - - -
341D ILE* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 3.5 40.6 - - + +
30D ILE* 3.8 35.9 - - + -
37D ALA* 4.4 6.7 - - + -
38D ARG* 1.3 75.8 - - - +
40D ALA* 1.3 60.7 + - - +
41D CYS* 4.0 15.5 - - + -
55D GLU 4.2 1.3 - - - -
56D ILE* 4.0 13.9 - - + -
264D GLY 2.9 24.7 - - - +
265D LYS* 3.0 14.9 - - - -
266D ASP* 2.8 9.0 + - - -
269D LYS* 3.1 8.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C PPK 5.9 1.6 - - - +
685C SAM 3.3 39.5 - - - +
38D ARG 4.1 0.2 + - - -
39D VAL* 1.3 73.2 - - - +
41D CYS* 1.3 58.8 + - - +
42D GLU* 4.0 5.5 + - + +
54D GLY* 3.4 5.2 - - - -
55D GLU* 2.9 44.4 + - + +
264D GLY 3.5 2.7 - - - -
265D LYS* 4.7 4.5 - - + +
269D LYS* 4.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D SER* 3.0 29.9 + - - +
26D VAL* 4.5 9.9 - - + -
39D VAL* 4.0 13.2 - - + -
40D ALA* 1.3 71.2 - - - +
42D GLU* 1.3 70.5 + - - +
43D THR* 4.2 7.2 - - - -
52D VAL* 3.5 32.1 - - - -
53D GLY 3.4 7.4 - - - +
56D ILE* 4.3 11.0 - - + -
95D ILE* 5.7 0.4 - - - -
263D SER 4.3 0.3 - - - +
264D GLY* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 2.6 32.0 + - - +
239C CYS* 3.8 30.7 - - + +
241C LEU* 4.0 12.6 - - + +
244C ARG* 3.0 41.5 + - - -
684C PPK 4.4 1.4 + - - -
686C K 3.0 19.8 - - - -
40D ALA 4.0 5.1 + - - +
41D CYS* 1.3 77.3 - - - +
43D THR* 1.3 61.4 + - - +
53D GLY 2.8 24.9 + - - +
242D THR* 3.3 16.0 - - - +
263D SER 4.9 1.6 - - - +
265D LYS* 5.3 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 4.3 0.9 - - - -
19D ALA* 3.7 9.6 - - - +
22D ILE* 3.9 23.5 - - + +
23D SER* 2.8 24.4 + - - -
41D CYS* 4.2 0.3 - - - -
42D GLU* 1.3 75.2 + - - +
44D TYR* 1.3 59.2 + - - +
45D VAL* 4.1 11.0 - - + -
50D VAL* 4.0 13.9 - - + -
51D LEU 3.0 18.8 - - - +
52D VAL* 4.1 9.0 - - + +
241D LEU* 3.4 8.1 - - - +
242D THR* 2.8 41.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 2.7 29.5 + - + -
44C TYR* 3.5 37.2 - + + -
51C LEU* 3.7 26.7 - - + -
53C GLY* 3.2 24.1 + - - -
94C ALA* 5.3 0.9 - - + -
43D THR* 1.3 72.3 - - - +
45D VAL* 1.3 64.6 + - - +
46D LYS* 4.5 6.0 + - + -
49D MET* 4.0 17.7 - - + +
50D VAL* 3.5 1.9 - - - -
51D LEU* 2.6 52.2 + - + +
239D CYS* 3.6 19.8 - - - -
240D GLY 3.7 3.1 - - - -
241D LEU* 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PRO 4.6 2.0 - - - +
18D ILE* 4.3 14.4 - - + -
19D ALA* 4.1 22.2 - - + +
22D ILE* 5.0 0.4 - - + -
43D THR* 4.1 16.6 - - + -
44D TYR* 1.3 80.9 - - - +
46D LYS* 1.3 65.5 + - - +
49D MET 3.4 14.6 - - - +
50D VAL* 3.7 16.2 - - + -
84D PHE* 3.9 2.9 - - + -
235D PRO* 3.6 25.2 - - + +
239D CYS* 3.6 5.4 - - - -
240D GLY* 2.7 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY* 3.6 13.4 + - - +
55C GLU* 2.9 31.5 + - - +
94C ALA* 4.1 21.8 - - + +
96C GLY* 4.6 8.4 - - - +
97C LYS 5.4 1.0 + - - -
44D TYR* 4.6 3.1 - - + -
45D VAL* 1.3 70.9 - - - +
47D THR* 1.3 96.0 + - + +
48D GLY 2.7 5.6 + - - -
49D MET* 2.9 43.0 + - + +
84D PHE* 3.1 4.5 - - - -
235D PRO* 3.1 30.0 + - - +
236D MET 3.5 8.9 + - - -
239D CYS* 3.6 28.3 - - - +
----------------------------------------------------------
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