Contacts of the helix formed by residues 25 - 40 (chain A) in PDB entry 3VA2
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 PRO 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE* 1.3 96.2 - - + +
26A THR* 1.3 66.3 + - - +
27A SER* 3.2 9.9 - - - +
28A ALA* 3.0 21.6 + - + +
29A LEU* 2.9 17.8 + - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE 3.4 3.9 + - - -
25A PRO* 1.3 70.9 - - - +
27A SER* 1.3 61.1 + - - +
29A LEU* 3.1 17.8 + - + +
30A VAL* 3.1 30.4 + - + +
94A ILE* 5.7 2.0 - - + -
97A TYR* 3.6 51.1 - - + +
126B MET* 5.7 0.7 - - - -
132B ILE* 3.6 22.2 - - + +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO* 4.5 9.0 + - - +
26A THR* 1.3 77.8 - - - +
28A ALA* 1.3 68.1 + - - +
30A VAL* 3.5 4.0 + - - +
31A LYS* 3.3 30.2 + - - +
127B ASN* 4.5 7.8 - - - +
132B ILE* 4.2 23.8 - - - +
178C TRP* 6.3 2.9 - - - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE 4.9 4.0 - - - +
25A PRO* 3.0 27.9 + - + +
27A SER* 1.3 81.0 + - - +
29A LEU* 1.3 64.8 + - - +
31A LYS* 3.6 9.7 + - - +
32A GLU* 3.1 26.2 + - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 5.0 16.1 - - - +
25A PRO 2.9 12.4 + - - +
26A THR* 3.1 21.5 + - + +
28A ALA* 1.3 78.2 - - - +
30A VAL* 1.3 53.4 + - - +
32A GLU* 3.4 10.1 + - - +
33A THR* 2.4 41.2 + - - +
90A ASN* 3.7 35.7 - - + +
93A LEU* 3.6 37.9 - - + +
94A ILE* 3.7 23.8 - - + +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.1 20.1 + - + +
27A SER* 3.9 4.9 - - - +
29A LEU* 1.3 72.9 - - - +
31A LYS* 1.3 59.5 + - - +
33A THR* 3.7 5.7 - - - -
34A LEU* 2.9 35.2 + - + +
94A ILE* 4.0 20.0 - - + -
123B LEU* 3.3 36.1 - - + +
126B MET* 4.0 23.3 - - + -
127B ASN* 3.8 19.5 - - + +
132B ILE* 5.0 4.9 - - + -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.3 20.0 + - - +
28A ALA* 3.9 8.3 - - - +
29A LEU 3.4 0.2 - - - -
30A VAL* 1.3 80.4 - - - +
32A GLU* 1.3 61.4 + - - +
34A LEU* 3.9 7.1 + - - +
35A ALA* 3.6 16.6 + - - +
127B ASN* 3.8 28.7 - - - +
146C LEU* 5.9 6.1 - - - +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE 5.6 3.8 + - - -
28A ALA 3.1 19.7 + - - +
29A LEU* 3.6 10.0 - - - +
31A LYS* 1.3 74.5 - - - +
33A THR* 1.3 65.9 + - - +
35A ALA* 3.1 15.3 + - - +
36A LEU* 3.1 29.3 + - + +
86A ARG* 3.3 35.3 + - - +
90A ASN* 3.6 16.8 + - - +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 2.4 31.2 + - - +
30A VAL* 3.7 4.0 - - - -
32A GLU* 1.3 72.7 - - - +
34A LEU* 1.3 58.3 + - - +
36A LEU* 3.5 4.8 + - - +
37A LEU* 2.9 27.8 + - - +
87A LEU* 3.7 14.0 - - + +
90A ASN* 3.2 32.4 - - + +
91A LEU* 3.6 30.5 - - + -
94A ILE* 3.7 14.7 - - + +
123B LEU* 4.2 7.0 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 2.9 22.9 + - + +
31A LYS* 3.9 6.7 - - - +
33A THR* 1.3 76.7 - - - +
35A ALA* 1.3 61.8 + - - +
37A LEU* 3.2 13.9 + - - +
38A SER* 3.2 14.2 + - - -
120B GLN* 3.4 38.9 - - + +
123B LEU* 3.8 45.0 - - + +
124B GLY* 4.2 7.2 - - - -
127B ASN* 4.4 13.2 - - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS 3.6 9.6 + - - +
32A GLU* 3.1 11.5 + - - +
34A LEU* 1.3 79.1 - - - +
36A LEU* 1.3 64.9 + - + +
38A SER* 2.6 24.9 + - - -
39A THR* 3.3 11.9 + - - -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.1 33.5 + - + +
33A THR 3.8 7.0 - - - +
35A ALA* 1.3 83.1 - - + +
37A LEU* 1.3 62.6 + - - +
39A THR* 3.2 7.3 + - - -
40A HIS* 3.2 35.2 + - + +
83A THR* 4.2 9.4 - - - +
86A ARG* 3.5 53.2 - - + +
87A LEU* 3.8 22.3 - - + +
90A ASN* 4.1 9.9 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR 2.9 13.4 + - - +
34A LEU* 3.4 7.4 - - - +
35A ALA 3.2 0.2 - - - -
36A LEU* 1.3 78.6 - - - +
38A SER* 1.3 60.3 + - - +
39A THR 3.6 0.2 + - - -
40A HIS* 3.8 2.4 + - - +
41A ARG* 3.7 19.9 + - - +
44A LEU* 4.6 1.5 - - + +
87A LEU* 3.8 30.5 - - + +
91A LEU* 5.1 0.9 - - + -
116B LEU* 4.0 29.1 - - + +
119B LEU* 3.6 28.7 - - + -
120B GLN* 3.7 29.2 + - - +
123B LEU* 3.7 25.6 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 3.2 7.6 + - - -
35A ALA* 2.6 25.5 + - - -
37A LEU* 1.3 78.0 - - - +
39A THR* 1.3 65.2 + - - +
40A HIS 3.4 0.2 - - - -
41A ARG* 3.2 40.7 - - - +
120B GLN* 4.4 5.6 - - - +
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 3.3 12.0 + - - -
36A LEU* 3.2 10.9 + - - -
38A SER* 1.3 82.1 + - - +
40A HIS* 1.3 75.7 + - + +
41A ARG* 3.2 4.4 + - - +
42A THR* 5.0 1.9 + - - -
83A THR* 5.6 0.2 - - - +
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.2 31.8 + - + +
37A LEU 3.8 4.5 + - - -
39A THR* 1.3 92.1 - - + +
41A ARG* 1.3 64.7 + - - +
42A THR 3.6 1.1 - - - -
43A LEU* 4.0 20.3 - - + +
44A LEU* 3.3 31.6 + - + +
82A GLY* 5.6 0.4 - - - -
83A THR* 2.6 43.3 + - - -
84A VAL* 3.3 36.3 - - + +
87A LEU* 4.8 8.1 - - + -
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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