Contacts of the helix formed by residues 26 - 40 (chain A) in PDB entry 1VCN
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 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 3.2 0.8 + - - -
25A LEU* 1.3 80.4 - - - +
27A LYS* 1.3 63.5 + - - +
28A GLY 3.2 2.5 - - - -
29A ILE* 3.3 14.6 + - - +
30A LEU* 3.0 20.8 + - - +
185A LEU* 4.2 1.7 - - - +
620A SO4 2.7 20.0 + - - -
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Residues in contact with LYS 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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17A ILE* 3.6 23.1 - - + +
18A THR* 3.5 17.9 - - - +
19A GLY* 3.3 28.7 - - - +
25A LEU 3.6 0.8 - - - -
26A GLY* 1.3 74.6 - - - +
28A GLY* 1.3 55.6 + - - +
30A LEU* 3.4 3.9 - - + +
31A THR* 2.7 37.8 + - - -
151A GLU* 2.6 40.3 + - + +
152A VAL 2.9 24.0 + - - -
153A GLY* 4.3 0.2 - - - -
154A GLY 4.7 4.1 + - - -
185A LEU* 3.2 29.4 - - + -
610A SO4 3.3 13.7 + - - -
620A SO4 3.0 12.4 + - - +
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Residues in contact with GLY 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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26A GLY 3.2 1.0 - - - -
27A LYS* 1.3 79.0 - - - +
29A ILE* 1.3 55.0 + - - +
31A THR* 3.3 3.3 + - - -
32A SER* 2.7 36.7 + - - -
81A ASP* 3.7 22.0 - - - -
84A HIS* 5.0 3.4 - - - -
85A TYR* 3.9 3.0 - - - -
151A GLU* 3.5 16.2 + - - -
620A SO4 3.2 9.3 + - - -
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Residues in contact with ILE 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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26A GLY* 3.3 14.2 + - - +
28A GLY* 1.3 72.8 - - - +
30A LEU* 1.3 57.6 + - - +
32A SER* 3.5 2.4 - - - -
33A SER* 2.7 51.4 + - - +
84A HIS* 3.6 38.6 - - + +
88A PHE* 4.3 20.6 - - + -
255A LEU* 4.4 15.3 - - + +
258A VAL* 3.9 26.2 - - + -
620A SO4 4.8 0.6 + - - +
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Residues in contact with LEU 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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17A ILE* 4.1 26.7 - - + -
26A GLY 3.0 14.5 + - - +
27A LYS* 3.4 7.9 - - + +
28A GLY 3.2 0.2 - - - -
29A ILE* 1.3 74.0 - - - +
31A THR* 1.3 66.3 + - - +
33A SER* 3.9 3.5 - - - -
34A LEU* 3.0 25.3 + - + +
183A LEU* 5.3 5.6 - - + -
184A HIS 6.0 0.2 - - - -
185A LEU* 4.0 26.7 - - + +
220A VAL* 4.0 36.3 - - + -
249A SER* 5.8 2.9 - - - +
258A VAL* 5.5 1.3 - - - -
262A LEU* 3.9 24.7 - - + -
267A LEU* 4.4 10.1 - - + -
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Residues in contact with THR 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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17A ILE* 3.8 16.2 - - + +
27A LYS 2.7 21.5 + - - -
28A GLY 3.5 4.9 - - - -
30A LEU* 1.3 77.6 - - - +
32A SER* 1.3 63.3 + - - +
34A LEU* 3.3 2.3 + - - +
35A GLY* 3.0 20.8 + - - -
47A ALA* 4.5 3.8 - - + -
85A TYR* 3.7 26.9 - - + +
149A VAL* 3.5 33.4 - - + +
151A GLU* 3.2 26.1 + - + +
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Residues in contact with SER 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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28A GLY 2.7 21.6 + - - -
29A ILE* 3.5 7.0 - - - -
31A THR* 1.3 76.5 - - - +
33A SER* 1.3 56.9 + - - +
35A GLY* 3.2 3.2 + - - -
36A ALA* 3.0 28.1 + - - +
84A HIS* 3.4 22.5 - - - +
85A TYR* 3.4 14.7 - - - +
88A PHE* 3.4 38.3 - - - +
89A LEU* 4.4 3.7 - - - +
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 2.7 29.4 + - - +
30A LEU 3.9 0.7 - - - -
32A SER* 1.3 69.9 - - - +
34A LEU* 1.3 66.1 + - - +
36A ALA* 3.3 2.8 + - - +
37A LEU* 3.0 29.1 + - - +
88A PHE* 3.9 8.0 - - - -
258A VAL* 3.1 18.8 - - - +
259A PRO* 3.5 25.0 - - - +
262A LEU* 3.8 24.0 - - - -
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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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15A VAL* 3.6 33.0 - - + -
17A ILE* 4.3 14.1 - - + -
30A LEU* 3.0 19.7 + - + +
31A THR* 3.8 4.3 - - - +
33A SER* 1.3 76.0 - - - +
35A GLY* 1.3 63.0 + - - +
37A LEU* 3.2 14.1 + - + +
38A LEU* 3.0 39.7 + - + +
149A VAL* 4.4 6.1 - - + -
183A LEU* 4.3 10.8 - - + -
262A LEU* 5.1 0.6 - - - +
267A LEU* 4.5 21.1 - - + +
268A GLY* 5.3 2.0 - - - -
271A VAL* 3.8 27.6 - - + -
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Residues in contact with GLY 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 THR 3.0 13.7 + - - -
32A SER 3.6 3.6 - - - -
34A LEU* 1.3 79.0 - - - +
36A ALA* 1.3 55.7 + - - +
38A LEU* 3.1 5.7 + - - +
39A ARG* 3.0 30.5 + - - +
45A VAL* 4.1 14.2 - - - +
89A LEU* 3.6 17.0 - - - +
149A VAL* 4.4 8.9 - - - +
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Residues in contact with ALA 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 SER 3.0 16.3 + - - +
33A SER* 3.7 5.6 - - - +
35A GLY* 1.3 75.9 - - - +
37A LEU* 1.3 58.8 + - - +
39A ARG* 3.1 7.7 + - - +
40A ALA* 2.8 30.3 + - - +
88A PHE* 3.9 22.7 - - + +
89A LEU* 3.8 6.4 - - - +
259A PRO* 4.9 3.8 - - + -
284A LEU* 5.8 0.2 - - - -
287A TRP* 4.1 27.6 + - + +
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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 SER 3.0 11.3 + - - +
34A LEU* 3.2 19.5 + - + +
36A ALA* 1.3 77.4 - - - +
38A LEU* 1.3 62.2 + - + +
40A ALA* 3.7 9.9 + - - +
41A ARG* 2.9 31.3 + - - +
259A PRO* 3.3 43.1 - - + +
262A LEU* 4.3 11.4 - - + -
263A GLU* 3.2 39.7 - - + +
267A LEU* 5.1 2.7 - - + -
268A GLY* 4.4 12.1 - - - +
284A LEU* 4.1 16.2 - - + -
287A TRP* 6.0 1.1 - - + -
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Residues in contact with LEU 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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15A VAL* 4.9 0.7 - - + -
34A LEU* 3.0 37.8 + - + +
35A GLY* 3.5 7.6 - - - +
36A ALA 3.1 0.2 - - - -
37A LEU* 1.3 77.0 - - + +
39A ARG* 1.3 65.0 + - - +
41A ARG* 3.1 30.8 + - - +
43A TYR* 3.5 17.3 + - + -
45A VAL* 3.7 13.7 - - + -
147A ILE* 3.8 42.8 - - + -
149A VAL* 4.1 13.2 - - + -
268A GLY* 5.7 2.9 - - - +
271A VAL* 4.4 21.1 - - + -
272A GLU* 5.6 3.4 - - + +
275A LEU* 5.2 1.1 - - + -
277A LEU* 5.4 2.9 - - + -
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Residues in contact with ARG 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 GLY 3.0 20.0 + - - +
36A ALA* 3.1 7.4 + - - +
38A LEU* 1.3 73.0 - - - +
40A ALA* 1.3 52.4 + - - +
41A ARG 2.7 6.4 + - - -
42A GLY* 2.6 28.2 + - - -
43A TYR 3.9 14.3 + - - +
45A VAL* 4.0 21.5 + - + +
88A PHE 4.6 6.0 + - - -
89A LEU* 3.4 49.8 + - + +
90A ASP* 4.8 10.3 + - - +
91A MET* 5.7 2.6 - - - -
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Residues in contact with ALA 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 ALA 2.8 15.4 + - - +
37A LEU 3.8 5.8 - - - +
38A LEU 3.3 0.2 - - - -
39A ARG* 1.3 74.3 - - - +
41A ARG* 1.3 57.2 + - - +
42A GLY 3.4 1.6 - - - -
281A ILE 4.2 1.7 - - - +
282A PRO* 3.3 4.4 - - + +
283A ASN* 2.9 52.8 + - - +
284A LEU* 3.4 23.3 - - + -
287A TRP* 5.9 2.9 - - + +
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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