Contacts of the helix formed by residues 19 - 36 (chain B) in PDB entry 3A3K
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 SER 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.8 8.7 - - - -
13B ASN 2.6 28.3 + - - -
14B THR* 3.5 11.8 - - - -
16B TYR* 3.0 42.1 + - - +
17B PRO 3.4 0.6 - - - -
18B TRP* 1.3 79.4 - - - +
20B TRP* 1.3 61.2 + - - +
21B ALA* 3.3 4.9 - - - -
22B ARG* 3.0 11.4 + - - +
23B VAL* 2.9 22.5 + - - +
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Residues in contact with TRP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.7 28.0 - - + -
9B LEU* 4.2 10.9 - - + +
10B PRO* 2.9 21.5 + - - +
11B LEU* 3.9 32.5 - - + +
18B TRP 3.6 1.8 + - - -
19B SER* 1.3 66.7 - - - +
21B ALA* 1.3 61.6 + - - +
22B ARG 3.0 2.0 - - - -
23B VAL* 4.3 10.8 - - + -
24B GLY* 2.7 58.7 + - - +
25B PRO* 3.5 1.2 - - - +
27B VAL* 4.6 4.3 - - + -
48B MET* 3.3 31.4 - - + -
50B LEU* 3.5 35.4 - - + +
82B LEU* 4.9 0.7 - - + -
305B PHE* 3.7 23.5 - + - -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO 4.8 0.4 + - - -
11B LEU 5.4 2.2 + - - -
13B ASN 5.6 0.2 + - - -
14B THR* 3.8 25.8 - - + -
19B SER* 3.3 2.5 - - - -
20B TRP* 1.3 78.0 - - - +
22B ARG* 1.3 58.0 + - + +
25B PRO* 3.3 17.7 - - - +
301B ALA* 4.1 6.6 - - - +
305B PHE* 4.3 17.9 - - - +
307B PHE* 3.8 39.1 - - + -
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.2 19.0 + - - -
15B SER 4.5 3.4 + - - -
16B TYR 2.8 29.8 + - - +
17B PRO* 3.8 27.3 - - - +
19B SER* 3.0 10.5 + - - +
21B ALA* 1.3 77.4 - - + +
23B VAL* 1.3 62.9 + - - +
24B GLY 3.4 1.6 - - - -
25B PRO* 3.4 13.9 - - - +
26B ALA 3.5 0.3 + - - -
297B LEU* 3.4 18.6 - - + +
307B PHE* 4.0 31.1 - - + -
309B VAL* 4.3 13.0 - - + +
310B GLU* 5.6 8.7 + - - +
314B LYS* 4.7 21.7 - - - +
315B ASN* 4.3 13.8 + - - +
318B PRO* 3.7 21.3 - - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.8 19.1 - - + -
17B PRO 4.3 1.8 - - - +
18B TRP* 3.4 37.2 - - - +
19B SER 2.9 10.6 + - - +
20B TRP* 4.3 4.0 - - + -
22B ARG* 1.3 75.3 - - - +
24B GLY* 1.3 60.2 + - - +
26B ALA* 3.2 6.4 + - - +
27B VAL* 2.8 37.8 + - + +
82B LEU* 4.7 0.4 - - + -
318B PRO* 4.2 8.5 - - + -
321B PHE* 3.6 44.4 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 2.7 52.4 + - - -
23B VAL* 1.3 71.8 - - - +
25B PRO* 1.4 65.7 - - - +
27B VAL* 3.2 4.7 + - - +
28B GLU* 3.0 22.0 + - - +
48B MET* 5.6 0.2 - - - +
305B PHE* 3.6 9.2 - - - -
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP 3.5 3.6 - - - +
21B ALA 3.3 26.7 - - - +
22B ARG* 3.4 12.6 - - - +
24B GLY* 1.4 87.0 - - - +
26B ALA* 1.3 60.2 + - - +
28B GLU* 3.3 1.4 + - + -
29B LEU* 3.1 28.3 + - - +
297B LEU* 3.9 13.2 - - + +
300B LEU* 3.4 21.4 - - + +
301B ALA* 4.0 20.6 - - + +
305B PHE* 3.5 30.0 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG 3.5 6.2 + - - +
23B VAL* 3.2 10.4 + - + +
25B PRO* 1.3 77.8 - - - +
27B VAL* 1.3 62.7 + - + +
29B LEU* 3.4 2.4 + - - +
30B ALA* 3.2 17.3 + - - +
293B PHE* 3.8 13.5 - - + -
297B LEU* 3.5 22.3 - - + +
318B PRO* 3.4 28.9 - - + +
322B HIS* 3.3 17.7 - - + +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 4.6 2.9 - - + -
23B VAL* 2.8 27.1 + - + +
24B GLY 3.7 4.7 - - - +
26B ALA* 1.3 73.5 - - - +
28B GLU* 1.3 59.6 + - - +
30B ALA* 3.1 9.1 + - - +
31B LEU* 2.9 31.7 + - + +
48B MET* 3.1 40.4 - - + -
82B LEU* 3.7 26.5 - - + -
321B PHE* 4.9 11.4 - - + +
322B HIS* 5.4 0.4 - - - +
325B LEU* 3.7 19.1 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.0 12.6 + - - +
25B PRO* 3.3 8.7 + - + +
27B VAL* 1.3 76.8 - - - +
29B LEU* 1.3 55.5 + - - +
31B LEU* 3.3 9.9 + - + +
32B ALA* 2.8 30.2 + - + +
300B LEU* 3.5 27.2 - - + +
304B LYS* 3.3 40.8 + - - +
305B PHE* 3.7 10.7 - - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO 3.1 19.0 + - - +
26B ALA* 3.6 6.5 - - - +
27B VAL 3.2 0.2 - - - -
28B GLU* 1.3 71.5 - - - +
30B ALA* 1.3 65.8 + - - +
32B ALA* 3.4 9.9 + - + +
33B ARG* 3.1 22.9 + - - +
293B PHE* 3.9 22.7 - - + -
296B GLN* 4.0 34.3 - - + +
297B LEU* 3.9 30.3 - - + +
300B LEU* 3.8 17.5 - - + -
322B HIS* 4.1 11.1 + - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.2 12.6 + - - +
27B VAL* 3.1 11.8 + - - +
29B LEU* 1.3 77.0 - - - +
31B LEU* 1.3 57.1 + - - +
33B ARG* 3.3 7.0 + - - +
34B VAL* 3.1 31.3 + - - +
322B HIS* 3.7 32.9 - - + +
325B LEU* 4.1 18.6 - - + -
326B LEU* 3.9 11.7 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 2.9 27.5 + - + +
28B GLU* 3.7 7.9 - - + +
30B ALA* 1.3 74.2 - - - +
32B ALA* 1.3 66.2 + - - +
34B VAL* 3.2 10.3 + - + +
35B LYS* 3.0 25.7 + - - +
46B VAL* 3.6 44.0 - - + +
48B MET* 3.9 28.9 - - + -
325B LEU* 4.1 17.3 - - + -
329B VAL* 5.8 0.4 - - + -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 2.8 20.9 + - + +
29B LEU* 3.6 12.3 - - + +
31B LEU* 1.3 75.2 - - - +
33B ARG* 1.3 62.7 + - - +
35B LYS* 3.3 11.3 + - - +
36B ALA* 3.2 21.4 + - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU 3.1 13.7 + - - +
30B ALA* 3.5 9.6 - - - +
31B LEU 3.3 0.2 - - - -
32B ALA* 1.3 76.2 - - - +
34B VAL* 1.3 62.1 + - - +
36B ALA* 3.3 13.8 + - - +
37B ARG* 3.4 32.2 + - + +
40B LEU* 5.7 1.6 - - + -
289B GLU* 6.3 0.6 - - - +
322B HIS* 3.7 10.7 + - - -
326B LEU* 3.9 30.9 - - - +
358B GLN 5.6 2.0 + - - -
359B GLY* 5.6 7.3 - - - -
360B VAL* 3.7 27.7 - - - +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA* 3.1 17.9 + - + +
31B LEU* 3.2 14.8 + - + +
33B ARG* 1.3 72.2 - - - +
35B LYS* 1.3 60.3 + - - +
37B ARG 2.8 35.0 + - - +
40B LEU* 4.4 19.9 - - + +
41B LEU* 4.4 15.3 - - + -
46B VAL* 4.8 7.0 - - + -
325B LEU* 6.3 0.4 - - + -
326B LEU* 3.7 20.4 - - + -
329B VAL* 4.0 32.8 - - + -
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU 3.0 17.2 + - - +
32B ALA* 3.6 9.0 - - - +
34B VAL* 1.3 77.8 - - - +
36B ALA* 1.3 59.3 + - + +
37B ARG 3.2 3.3 + - - -
38B PRO* 4.7 5.4 - - - +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA 3.2 14.8 + - - +
33B ARG* 3.9 6.3 - - - +
34B VAL 3.0 1.6 + - - -
35B LYS* 1.3 76.9 - - + +
37B ARG* 1.3 64.5 + - + +
38B PRO* 3.5 11.0 - - - +
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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
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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) + - + + + + + -
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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