Contacts of the helix formed by residues 22 - 38 (chain Q) in PDB entry 1VYH
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 ASP 22 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q ASP* 3.5 24.8 + - - +
20Q GLY 3.3 5.9 - - - +
21Q ASP* 1.3 81.4 + - - +
23Q ARG* 1.3 60.3 + - - +
24Q TRP 3.5 1.1 - - - -
25Q MET* 3.1 29.9 + - - +
26Q SER* 3.4 17.7 + - - -
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Residues in contact with ARG 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ASP* 5.2 2.4 - - - +
19Q GLN* 3.3 32.1 + - - +
21Q ASP* 3.1 30.3 + - - +
22Q ASP* 1.3 76.1 - - - +
24Q TRP* 1.3 66.5 + - - +
26Q SER* 3.2 5.5 - - - -
27Q GLN* 3.2 33.5 + - - +
143R GLY* 4.4 6.1 - - - +
193R ASP* 3.0 48.2 + - - +
194R PHE* 3.4 31.0 - - + -
195R LEU* 3.8 23.1 - - - +
196R HIS* 5.4 1.8 + - - -
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Residues in contact with TRP 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q ALA* 3.8 13.7 - - + -
15Q ALA* 3.8 49.5 - - + +
17Q ASP* 5.8 7.3 - - + +
22Q ASP 3.5 0.4 - - - -
23Q ARG* 1.3 78.2 - - - +
25Q MET* 1.3 81.5 + - + +
27Q GLN* 3.2 11.9 + - - +
28Q HIS* 3.1 20.3 + - + +
73Q ILE* 3.8 19.9 - - + +
74Q GLY 5.4 1.1 - - - -
76Q ASP* 2.8 32.8 + - - -
80Q HIS* 4.1 13.9 - - + -
83Q TRP* 3.7 31.2 - + - -
84Q ARG* 3.6 28.3 - - + -
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Residues in contact with MET 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q ALA* 5.6 2.5 - - + -
15Q ALA 5.7 1.1 - - - +
22Q ASP* 3.1 24.4 + - - +
24Q TRP* 1.3 101.0 - - + +
26Q SER* 1.3 64.8 + - - +
28Q HIS* 3.7 20.7 - - + +
29Q ASN* 2.9 42.5 + - - +
83Q TRP* 4.2 18.4 - - + -
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Residues in contact with SER 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASP 4.9 0.3 + - - -
22Q ASP* 3.4 17.2 + - - -
23Q ARG* 3.2 15.0 - - - -
25Q MET* 1.3 78.0 - - - +
27Q GLN* 1.3 57.6 + - - +
29Q ASN* 3.4 9.0 + - - +
30Q ARG* 3.1 26.7 + - - +
144R GLU* 3.0 48.0 + - - +
145R LYS* 5.5 0.2 - - - +
194R PHE* 4.2 12.1 - - - -
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Residues in contact with GLN 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q ARG* 3.2 25.4 + - - +
24Q TRP* 3.6 6.1 - - - +
26Q SER* 1.3 78.7 - - - +
28Q HIS* 1.3 65.4 + - - +
30Q ARG* 3.2 15.9 + - - +
31Q PHE* 3.1 32.0 + - + -
51Q GLN* 3.0 32.6 + - - +
72Q GLY 4.3 0.3 - - - +
73Q ILE* 3.9 29.3 - - + +
192R PHE 3.9 3.1 - - - +
193R ASP* 3.2 30.4 + - - +
194R PHE* 3.8 20.0 - - + -
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Residues in contact with HIS 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q TRP* 3.1 16.3 + - + +
25Q MET* 3.7 22.9 - - + +
27Q GLN* 1.3 75.1 - - - +
29Q ASN* 1.3 73.2 + - - +
31Q PHE* 3.1 14.7 + - - +
32Q VAL* 3.0 34.6 + - + +
73Q ILE* 4.3 1.2 - - - +
83Q TRP* 4.0 22.1 - + - -
84Q ARG* 3.6 37.9 - - + +
87Q ASN* 3.6 21.1 + - - +
89Q GLU* 2.9 25.2 + - + -
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Residues in contact with ASN 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q MET* 2.9 36.6 + - - +
26Q SER* 3.6 7.6 - - - +
28Q HIS* 1.3 83.7 - - - +
30Q ARG* 1.3 56.2 + - - +
32Q VAL* 3.0 10.6 + - - +
33Q LEU* 2.7 36.3 + - - +
144R GLU* 5.8 1.3 - - - +
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Residues in contact with ARG 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q SER 3.1 14.0 + - - +
27Q GLN* 3.2 18.2 + - - +
29Q ASN* 1.3 74.8 - - - +
31Q PHE* 1.3 83.6 + - - +
33Q LEU* 3.3 24.0 - - + +
34Q ASP* 2.8 55.7 + - - +
51Q GLN* 5.6 2.0 - - - +
54Q GLN* 5.3 8.5 + - - +
69Q LEU* 5.8 3.6 - - - +
70Q ASN 4.9 3.6 + - - -
144R GLU* 4.9 6.5 + - - +
188R CYS* 3.4 38.7 - - - +
192R PHE 4.4 14.1 + - - -
194R PHE* 4.2 12.1 - - + -
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Residues in contact with PHE 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q GLN* 3.1 23.1 + - + -
28Q HIS* 3.3 12.8 - - - +
30Q ARG* 1.3 103.8 - - - +
32Q VAL* 1.3 54.8 + - - +
34Q ASP* 2.9 9.1 + - - +
35Q CYS* 2.6 35.5 + - - +
51Q GLN* 4.7 3.8 - - - -
70Q ASN 3.3 18.8 - - - -
71Q PHE* 3.5 34.6 - + + -
72Q GLY 3.5 20.9 - - - -
73Q ILE* 3.5 28.3 - - + -
84Q ARG* 3.9 0.4 - - - -
89Q GLU* 3.7 31.0 - - + -
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Residues in contact with VAL 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 3.0 45.0 + - + +
29Q ASN* 3.0 10.6 + - - +
31Q PHE* 1.3 73.9 - - - +
33Q LEU* 1.3 63.7 + - - +
35Q CYS* 2.9 20.3 + - + +
36Q LYS* 3.1 15.3 + - + +
87Q ASN 4.1 6.3 - - - +
88Q GLY* 4.0 21.8 - - - +
89Q GLU* 4.6 2.5 - - + -
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Residues in contact with LEU 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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29Q ASN 2.7 11.8 + - - +
30Q ARG* 3.3 30.3 - - + +
32Q VAL* 1.3 76.8 - - - +
34Q ASP* 1.3 67.6 + - - +
36Q LYS* 3.0 29.0 + - - +
37Q ASP* 3.6 14.9 - - - +
151S ASP* 3.7 29.2 - - - +
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Residues in contact with ASP 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ARG* 2.8 41.1 + - - +
31Q PHE* 2.9 13.3 + - - +
33Q LEU* 1.3 83.3 - - - +
35Q CYS* 1.3 56.8 + - - +
37Q ASP* 4.9 2.8 - - - +
38Q LYS* 3.2 43.0 + - - +
69Q LEU* 4.3 29.9 - - + +
71Q PHE* 4.6 4.0 - - + -
93Q ILE* 4.8 0.3 - - - +
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Residues in contact with CYS 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 PHE 2.6 11.9 + - - +
32Q VAL* 2.9 15.7 + - + +
34Q ASP* 1.3 73.0 - - - +
36Q LYS* 1.3 60.6 + - - +
37Q ASP 3.5 0.6 + - - -
38Q LYS 4.4 1.0 - - - +
71Q PHE* 3.9 12.5 - - - -
88Q GLY 4.0 5.6 - - - +
89Q GLU* 3.4 36.8 - - - -
91Q GLU 3.4 22.5 - - - +
92Q ASN* 3.4 20.2 + - - +
93Q ILE* 3.6 31.4 - - - +
212S ARG* 5.1 0.2 + - - -
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Residues in contact with LYS 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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32Q VAL* 3.1 10.9 + - + +
33Q LEU* 3.0 20.9 + - - +
35Q CYS* 1.3 79.7 - - - +
37Q ASP* 1.3 63.9 + - + +
92Q ASN* 3.8 14.9 + - - +
151S ASP* 4.3 18.6 + - - -
170S ALA* 5.0 9.6 + - - -
172S MET* 6.2 2.4 - - - +
193S HIS* 3.8 19.3 + - + -
212S ARG* 2.6 28.3 + - - -
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Residues in contact with ASP 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q LEU* 3.6 15.9 - - - +
34Q ASP* 3.8 3.1 + - - +
36Q LYS* 1.3 91.9 - - + +
38Q LYS* 1.3 74.6 + - - +
39Q GLU* 4.3 2.8 - - - +
151S ASP* 4.1 11.3 - - - +
152S SER* 5.3 4.8 - - - -
154S GLN* 6.3 0.2 - - - +
170S ALA* 3.7 21.4 - - - +
193S HIS* 5.3 1.3 - - - +
194S ASN* 3.5 23.5 + - + +
212S ARG* 3.4 8.7 - - - +
236S TRP* 4.3 13.4 - - + -
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Residues in contact with LYS 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 ASP* 3.2 29.8 + - - +
35Q CYS 4.4 0.7 - - - +
37Q ASP* 1.3 93.0 + - - +
39Q GLU* 1.3 68.2 + - - +
40Q PRO* 4.1 2.7 - - + -
69Q LEU* 4.0 23.6 - - + -
92Q ASN* 5.8 0.7 - - - +
93Q ILE* 3.6 15.2 - - - +
110S PRO* 5.8 2.6 - - - +
128S GLU* 3.4 29.5 + - - -
212S ARG* 4.4 6.8 + - - -
342S ARG* 5.6 5.8 - - - +
382S PHE* 6.0 4.8 - - - -
400S VAL* 5.9 4.6 - - - +
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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