Contacts of the strand formed by residues 2 - 20 (chain B) in PDB entry 3QLD
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 LEU 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 1.3 75.6 - - - +
3B GLN* 1.3 60.2 + - - +
35B LEU* 4.5 18.2 - - + -
36B VAL 4.3 8.3 - - - +
37B ASP* 4.0 7.2 - - + +
75B PHE* 3.9 26.7 - - + -
79B LEU* 4.1 21.6 - - + +
88B VAL* 4.3 20.5 - - + +
114B VAL* 4.6 2.7 - - + -
117B TRP* 3.6 49.6 - - + +
376B LEU* 4.1 22.8 - - + +
377B ARG* 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 3.2 5.7 + - - +
2B LEU* 1.3 74.5 - - - +
4B THR* 1.4 64.8 + - - +
36B VAL* 2.9 14.7 + - + +
37B ASP 4.2 6.3 - - - +
38B ALA* 3.7 31.7 - - - +
375B ASP* 3.3 9.0 - - - +
376B LEU* 2.8 31.3 + - - -
377B ARG* 3.4 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 1.4 90.6 + - - +
5B CYS* 1.3 64.9 + - - +
6B VAL* 3.6 27.1 - - + -
34B GLN 3.9 0.5 - - - +
35B LEU* 3.4 4.2 - - - -
36B VAL* 2.9 44.5 + - + +
373B SER* 4.4 7.4 - - - +
374B VAL 3.5 10.9 + - - +
375B ASP* 4.9 2.6 - - - +
376B LEU* 3.8 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 1.3 73.2 - - - +
6B VAL* 1.3 61.5 + - - +
7B LEU* 3.9 26.2 - - - -
33B VAL* 4.2 7.6 - - - -
34B GLN 3.5 2.7 - - - -
35B LEU* 3.9 21.8 - - + -
72B VAL* 4.0 24.7 - - + -
75B PHE* 5.4 2.7 - - + -
110B ILE* 6.0 1.8 - - - -
372B TRP* 4.0 2.0 - - - +
373B SER* 3.1 4.7 - - - -
374B VAL* 3.0 31.3 + - - +
376B LEU* 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 3.6 20.2 - - + -
5B CYS* 1.3 76.1 - - - +
7B LEU* 1.3 65.5 + - - +
8B HIS* 3.4 26.4 - - + +
32B LEU 3.7 0.3 - - - +
33B VAL* 3.7 2.6 - - - -
34B GLN* 2.8 58.3 + - - +
36B VAL* 5.0 3.6 - - + -
371B THR* 3.8 18.2 - - + -
372B TRP 3.4 4.9 - - - +
373B SER* 3.8 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B CYS* 3.9 18.8 - - - -
6B VAL* 1.3 73.1 - - - +
8B HIS* 1.3 61.1 + - - +
31B ILE* 4.7 2.9 - - + -
32B LEU 3.6 2.7 - - - +
33B VAL* 3.8 27.4 - - + -
64B TRP* 3.6 23.1 - - + -
67B LEU* 3.8 30.1 - - + -
68B VAL* 3.7 31.4 - - + +
72B VAL* 4.7 2.9 - - + -
110B ILE* 6.4 0.2 - - + -
371B THR* 3.3 8.3 - - - +
372B TRP* 2.7 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.4 25.3 - - + +
7B LEU* 1.3 72.9 - - - +
9B ARG* 1.3 60.7 + - - +
10B LEU* 3.6 20.1 + - + +
30B ALA 3.7 0.3 - - - +
31B ILE* 3.3 3.7 - - - +
32B LEU* 2.8 51.3 + - + +
34B GLN* 2.7 31.8 + - + +
44B TRP* 3.7 24.2 - + - -
64B TRP* 4.0 3.1 - - - -
364B VAL* 4.0 14.3 - - + +
368B SER* 4.4 4.8 + - - +
370B ALA 3.7 4.5 - - - -
371B THR* 4.0 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B HIS* 1.3 73.7 - - - +
10B LEU* 1.3 60.0 + - - +
29B GLN* 2.4 37.0 + - - +
30B ALA 3.5 8.1 - - - +
31B ILE* 4.5 2.7 - - + +
60B THR* 3.7 22.4 + - + +
61B ASP* 3.0 39.6 + - - +
64B TRP* 3.7 34.1 - - + +
368B SER* 3.3 5.2 - - - -
369B THR* 2.8 47.1 + - - +
370B ALA* 2.9 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B HIS* 3.6 21.8 - - + +
9B ARG* 1.3 78.6 + - - +
11B SER* 1.3 63.1 + - - +
12B LEU* 4.0 13.9 - - + -
28B LYS 4.1 0.9 - - - -
29B GLN* 3.2 7.4 - - - +
30B ALA* 2.9 35.4 + - + +
32B LEU* 3.5 28.9 - - + -
301B THR* 5.2 2.9 - - + -
334B VAL* 3.7 24.5 - - + -
364B VAL* 3.9 11.0 - - + +
367B PHE* 3.3 20.4 - - + +
368B SER* 3.3 24.5 - - - +
369B THR* 4.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 1.3 74.3 + - - +
12B LEU* 1.3 59.7 + - - +
13B PRO* 4.1 1.0 - - - +
27B GLU* 3.2 26.7 - - - +
28B LYS 3.2 7.0 - - - -
29B GLN* 4.1 12.9 - - - +
367B PHE* 3.1 28.4 + - - +
369B THR* 3.7 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.0 31.9 - - + -
11B SER* 1.3 75.3 - - - +
13B PRO* 1.4 67.7 - - + +
14B LEU 3.4 0.2 + - - -
27B GLU* 3.3 3.2 - - - -
28B LYS* 2.7 43.7 + - + +
30B ALA* 5.6 0.2 - - + -
301B THR* 4.2 15.5 - - + -
330B PHE* 3.7 30.5 - - + -
332B GLN 3.6 20.0 - - - +
333B ASP* 3.9 22.4 - - - +
334B VAL* 4.3 5.8 - - + -
367B PHE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER 4.1 1.6 - - - +
12B LEU* 1.4 84.6 - - + +
14B LEU* 1.3 64.7 + - - +
15B LYS 3.7 1.2 + - - -
26B ARG 3.7 7.6 - - - +
27B GLU* 3.8 20.6 - - - +
330B PHE* 3.5 17.0 - - - +
331B GLU* 4.7 3.3 + - - +
332B GLN 5.4 1.7 + - - +
367B PHE* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 1.3 74.5 - - - +
15B LYS* 1.3 64.3 + - - +
16B PHE 4.1 8.7 - - - +
17B PRO* 3.9 15.6 - - - +
18B MSE 4.4 12.8 - - + -
25B ILE* 3.5 29.6 - - + +
26B ARG 2.9 14.7 + - - +
27B GLU 3.8 18.8 - - - +
28B LYS* 3.9 9.2 - - + +
299B TYR* 4.1 27.6 - - + -
329B TYR* 3.6 11.9 - - + +
330B PHE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO 3.7 2.6 + - - -
14B LEU* 1.3 71.4 - - - +
16B PHE* 1.3 94.9 + - + +
17B PRO* 3.5 6.6 - - - +
327B ASP* 3.1 38.9 + - - +
329B TYR 2.8 23.4 + - - +
330B PHE* 4.0 5.0 + - - +
331B GLU* 3.8 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.1 5.8 - - - +
15B LYS* 1.3 122.3 - - + +
17B PRO* 1.3 71.8 - - - +
18B MSE 3.4 13.9 + - - +
327B ASP 4.5 2.0 - - - -
328B ARG* 3.5 28.5 - - + -
329B TYR* 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.9 12.3 - - + +
15B LYS 3.5 8.5 - - - +
16B PHE* 1.3 89.8 - - - +
18B MSE 1.3 63.2 + - + +
19B ARG* 4.1 9.2 + - - +
24B HIS* 4.8 13.6 + - + +
25B ILE 3.3 17.7 - - - +
26B ARG* 4.2 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.4 13.7 - - + -
16B PHE 3.6 14.4 - - - +
17B PRO* 1.3 74.1 - - + +
19B ARG* 1.3 68.7 + - - +
24B HIS* 3.3 6.0 - - - -
25B ILE* 2.9 45.1 + - + +
299B TYR* 3.7 55.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 5.0 7.4 + - - +
18B MSE 1.3 79.4 - - - +
20B THR* 1.3 68.2 + - - +
23B GLY 3.8 5.4 - - - +
24B HIS* 3.9 21.6 - - + +
25B ILE* 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MSE 3.6 1.5 + - - +
19B ARG* 1.3 79.9 - - - +
21B ALA* 1.3 68.5 + - - +
22B HIS 3.6 3.1 + - - -
23B GLY 2.8 36.3 + - - +
24B HIS 3.6 1.7 + - - -
25B ILE* 3.3 43.5 - - + +
----------------------------------------------------------
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