Contacts of the helix formed by residues 21 - 31 (chain A) in PDB entry 1V72
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 1.3 74.1 - - - +
22A PRO* 1.3 66.5 - - - +
23A GLU* 3.5 15.5 - - - -
24A VAL* 2.8 37.4 + - - +
25A ALA* 3.6 3.3 + - - +
214A GLY 2.9 8.6 + - - -
261A LEU* 4.2 7.9 - - - -
265A ASN* 2.9 32.0 + - - -
332A PHE* 3.5 18.4 - - - -
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Residues in contact with PRO 22 (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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20A ALA 3.3 4.8 - - - +
21A SER* 1.3 84.2 - - - +
23A GLU* 1.3 75.7 + - - +
25A ALA* 3.6 7.0 + - + +
26A GLN* 3.0 34.4 + - + +
332A PHE* 5.7 0.4 - - + -
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Residues in contact with GLU 23 (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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21A SER* 3.5 9.0 - - - -
22A PRO* 1.3 95.9 - - - +
24A VAL* 1.3 60.6 + - - +
26A GLN* 4.0 6.5 - - - +
27A ALA* 3.1 22.7 + - - +
255A ALA* 3.8 8.9 - - + +
261A LEU* 4.1 33.5 - - + +
264A ARG* 4.5 10.7 + - - +
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Residues in contact with VAL 24 (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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21A SER* 2.8 21.3 + - - +
23A GLU* 1.3 75.8 - - - +
25A ALA* 1.3 64.7 + - - +
27A ALA* 2.9 15.1 + - - +
28A LEU* 3.2 12.0 + - - +
214A GLY 3.5 21.8 - - - +
215A VAL* 4.1 14.8 - - + -
216A LEU* 3.4 26.7 - - + -
252A GLN* 3.7 31.8 - - + +
255A ALA* 4.0 14.1 - - + -
256A TYR* 5.0 1.1 - - + +
261A LEU* 4.6 7.2 - - + -
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Residues in contact with ALA 25 (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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20A ALA* 5.7 3.4 - - + +
21A SER 3.6 4.1 + - - +
22A PRO* 3.6 9.3 + - + +
24A VAL* 1.3 79.8 - - - +
26A GLN* 1.3 65.0 + - + +
28A LEU* 3.1 25.2 + - + +
29A VAL* 3.1 18.0 + - + +
216A LEU* 4.4 9.7 - - + +
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Residues in contact with GLN 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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22A PRO* 3.0 27.3 + - + +
23A GLU* 4.0 7.0 - - - +
24A VAL 3.2 0.8 - - - -
25A ALA* 1.3 76.6 - - + +
27A ALA* 1.3 65.2 + - - +
29A VAL* 3.2 24.9 + - - +
30A LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 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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23A GLU 3.1 13.6 + - - +
24A VAL 2.9 11.0 + - - +
26A GLN* 1.3 76.7 - - - +
28A LEU* 1.3 57.1 + - - +
30A LYS* 3.3 6.3 + - - -
31A HIS* 3.0 40.7 + - + +
251A ALA* 3.6 28.3 - - + +
254A ASP* 6.0 1.3 - - - +
255A ALA* 4.0 8.5 - - + -
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Residues in contact with LEU 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 VAL 3.7 9.2 - - - +
25A ALA* 3.1 11.8 + - + +
27A ALA* 1.3 76.4 - - - +
29A VAL* 1.3 59.2 + - - +
31A HIS* 3.3 3.2 + - - +
32A SER* 2.6 35.8 + - - +
216A LEU* 4.1 29.8 - - + -
248A PHE* 3.4 43.2 - - + +
251A ALA* 3.9 16.8 - - + -
252A GLN* 4.0 12.1 - - + +
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Residues in contact with VAL 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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25A ALA* 3.1 15.1 + - + +
26A GLN* 3.4 27.1 - - - +
27A ALA 3.2 0.4 - - - -
28A LEU* 1.3 77.6 - - + +
30A LYS* 1.3 63.7 + - - +
32A SER* 3.2 20.3 + - - -
33A SER* 4.6 2.1 + - - -
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Residues in contact with LYS 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 GLN 3.0 12.5 + - - +
27A ALA* 3.6 10.3 - - - +
29A VAL* 1.3 80.0 - - - +
31A HIS* 1.3 86.3 + - + +
32A SER 3.6 0.7 + - - -
33A SER* 3.9 13.5 + - - +
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Residues in contact with HIS 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 ALA* 3.0 31.4 + - + +
28A LEU 3.3 4.0 + - - +
29A VAL 3.2 0.4 - - - -
30A LYS* 1.3 108.3 + - + +
32A SER* 1.3 56.8 + - - +
33A SER 3.3 3.6 - - - -
44A LEU* 3.7 46.8 - - + +
247A ARG* 3.2 39.8 + - - +
248A PHE* 3.4 5.9 - - + -
251A ALA* 4.0 14.6 - - + -
254A ASP* 5.1 3.8 + - - -
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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