Contacts of the helix formed by residues 29 - 46 (chain Q) in PDB entry 5A31
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 GLY 29 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q PRO* 1.3 70.3 - - - +
31Q VAL 3.4 2.5 - - - -
32Q GLY* 3.5 7.1 + - - -
33Q LYS* 2.9 28.6 + - - +
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Residues in contact with PRO 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLY* 1.3 82.4 - - - +
31Q VAL* 1.3 72.7 + - + +
33Q LYS* 3.5 11.1 - - + +
34Q ARG* 3.0 28.2 + - - +
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Residues in contact with VAL 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLY 3.4 0.2 - - - -
30Q PRO* 1.3 85.3 - - + +
32Q GLY* 1.3 61.1 + - - +
34Q ARG* 3.3 7.8 - - - +
35Q LEU* 2.9 28.9 + - + +
60Q PHE* 3.7 24.5 - - + -
86Q PRO 5.4 1.6 - - - +
88Q GLY 5.8 2.5 - - - +
89Q TYR* 3.4 52.0 - - + +
90Q PRO* 4.7 4.7 - - + -
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Residues in contact with GLY 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLY* 3.5 10.5 + - - -
31Q VAL* 1.3 79.8 - - - +
33Q LYS* 1.3 55.4 + - - +
35Q LEU* 3.2 1.5 + - - -
36Q GLN* 2.9 27.6 + - - +
59Q LEU* 3.0 27.4 - - - +
60Q PHE* 4.1 17.4 - - - -
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Residues in contact with LYS 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS* 4.4 11.9 + - - +
28B MET* 4.8 11.6 - - - +
35B PRO* 5.2 14.2 - - - +
29Q GLY 2.9 18.3 + - - +
30Q PRO* 3.5 10.8 - - + +
31Q VAL 3.2 0.2 - - - -
32Q GLY* 1.3 75.9 - - - +
34Q ARG* 1.3 62.4 + - - +
36Q GLN* 3.2 10.5 + - + +
37Q GLN* 2.6 58.8 + - + +
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Residues in contact with ARG 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE 5.9 0.4 + - - -
30Q PRO 3.0 14.8 + - - +
31Q VAL* 3.3 13.2 - - - +
33Q LYS* 1.3 77.5 - - - +
35Q LEU* 1.3 57.2 + - - +
37Q GLN* 3.3 17.1 + - - +
38Q GLU* 2.5 53.3 + - - +
89Q TYR* 3.7 15.1 + - + -
90Q PRO* 3.3 33.2 - - + +
122Q TRP* 5.1 0.2 - - - -
124Q ALA* 2.9 26.2 + - - +
125Q LEU* 4.1 5.4 + - - +
126Q TYR 2.8 29.3 + - - -
127Q ASP* 5.1 0.6 - - - +
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Residues in contact with LEU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q VAL* 2.9 23.2 + - + +
32Q GLY 3.2 4.2 + - - +
34Q ARG* 1.3 70.9 - - - +
36Q GLN* 1.3 59.1 + - - +
38Q GLU* 4.1 11.4 - - - +
39Q LEU* 2.9 28.9 + - - +
59Q LEU* 3.3 35.4 - - + +
60Q PHE* 3.7 31.0 - - + -
62Q TRP* 3.7 14.0 - - + -
85Q PHE* 3.6 46.7 - - + -
89Q TYR* 3.7 15.5 - - + -
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Residues in contact with GLN 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757N TYR* 5.4 2.6 + - - -
779N MET 5.9 0.4 + - - -
780N PHE* 5.4 9.5 + - - +
784N GLY* 4.9 2.6 - - - -
785N PRO* 2.9 45.6 - - + +
32Q GLY 2.9 21.4 + - - +
33Q LYS* 3.2 11.6 + - - +
35Q LEU* 1.3 77.5 - - - +
37Q GLN* 1.3 58.4 + - + +
39Q LEU* 3.5 12.8 + - - +
40Q MET* 3.0 27.5 + - - +
59Q LEU* 3.4 24.1 - - + +
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Residues in contact with GLN 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS 4.7 4.3 + - - +
27B ARG* 4.6 21.5 - - - +
28B MET* 5.8 0.5 - - - +
33Q LYS* 2.6 52.7 + - + +
34Q ARG* 3.5 16.8 - - - +
36Q GLN* 1.3 76.1 - - + +
38Q GLU* 1.3 61.0 + - + +
40Q MET* 3.3 6.7 + - - +
41Q THR* 2.9 34.1 + - - +
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Residues in contact with GLU 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q ARG* 2.5 55.3 + - - +
35Q LEU* 3.8 13.6 - - + +
37Q GLN* 1.3 74.4 - - + +
39Q LEU* 1.3 58.3 + - - +
41Q THR* 3.7 6.8 - - - -
42Q LEU* 2.9 29.8 + - - +
62Q TRP* 4.4 2.5 - - + -
89Q TYR* 2.6 24.4 + - - -
127Q ASP* 3.4 25.2 - - + +
128Q VAL* 2.9 38.9 + - + +
129Q ARG* 5.6 1.4 + - - +
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Residues in contact with LEU 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757N TYR* 5.2 10.1 - - + +
35Q LEU 2.9 17.3 + - - +
36Q GLN* 3.5 13.5 - - - +
38Q GLU* 1.3 76.7 - - - +
40Q MET* 1.3 59.0 + - - +
42Q LEU* 3.2 4.2 + - + -
43Q MET* 2.9 51.5 + - + +
52Q ALA 4.1 2.2 - - - +
53Q PHE* 3.9 34.3 - - + -
54Q PRO* 3.8 25.6 - - + -
59Q LEU* 5.3 3.6 - - + -
62Q TRP* 3.7 26.8 - - + -
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Residues in contact with MET 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785N PRO* 5.7 9.2 - - - -
36Q GLN 3.0 17.6 + - - +
37Q GLN* 3.3 6.0 + - - +
39Q LEU* 1.3 76.9 - - - +
41Q THR* 1.3 58.1 + - - +
43Q MET* 3.2 8.5 + - + +
44Q MET* 2.9 52.8 + - + +
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Residues in contact with THR 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q GLN* 2.9 19.5 + - - +
38Q GLU* 3.7 7.6 - - - -
40Q MET* 1.3 74.6 - - - +
42Q LEU* 1.3 65.4 + - - +
44Q MET* 3.2 5.8 + - - +
45Q SER* 3.0 24.6 + - - -
127Q ASP* 3.9 18.8 - - - +
129Q ARG* 4.7 12.1 - - + -
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Residues in contact with LEU 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q GLU 2.9 17.9 + - - +
39Q LEU* 3.7 4.0 - - + +
41Q THR* 1.3 78.8 - - - +
43Q MET* 1.3 72.2 + - + +
45Q SER* 3.1 21.5 + - - +
46Q GLY* 4.0 3.1 + - - -
47Q ASP* 5.3 0.6 + - + -
50Q ILE* 4.0 26.2 - - + +
51Q SER* 5.1 3.8 - - - -
52Q ALA* 3.7 44.9 - - + +
62Q TRP* 4.6 5.2 - - + -
128Q VAL* 4.2 9.0 - - + -
129Q ARG* 3.8 31.6 - - + +
132Q LEU* 4.1 7.2 - - + -
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Residues in contact with MET 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756N THR* 5.4 12.3 - - + -
39Q LEU* 2.9 34.0 + - + +
40Q MET* 3.2 12.5 + - + +
42Q LEU* 1.3 90.9 - - + +
44Q MET* 1.3 68.2 + - + +
45Q SER 3.5 0.2 + - - -
46Q GLY* 4.3 4.7 + - - -
51Q SER* 4.9 8.3 - - - +
52Q ALA 3.8 21.8 - - - +
53Q PHE* 4.4 18.8 - - + -
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Residues in contact with MET 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q MET* 2.9 45.1 + - + +
41Q THR* 4.0 4.9 - - - +
43Q MET* 1.3 83.4 - - + +
45Q SER* 1.3 62.3 + - - +
46Q GLY* 3.4 1.2 + - - -
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Residues in contact with SER 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q THR* 3.0 16.3 + - - -
42Q LEU* 3.1 16.2 + - - +
44Q MET* 1.3 79.6 - - - +
46Q GLY* 1.3 63.0 + - - +
47Q ASP* 2.5 34.1 + - - +
129Q ARG* 3.4 18.4 + - - -
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Residues in contact with GLY 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q LEU 4.0 4.6 + - - -
43Q MET 4.3 4.1 + - - -
44Q MET 3.4 4.0 + - - -
45Q SER* 1.3 78.2 + - - +
47Q ASP* 1.3 63.5 + - - +
48Q LYS* 3.5 3.1 + - - +
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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
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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