Contacts of the helix formed by residues 29 - 36 (chain B) in PDB entry 2YEV
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B HIS 4.6 0.2 + - - -
28B GLY* 1.3 79.0 - - - +
30B SER* 1.3 65.7 + - - -
31B PHE 3.1 4.0 + - - -
32B ASN* 3.3 11.5 + - - +
33B GLN* 3.3 15.1 + - - +
168B GLY 4.0 0.6 + - - -
169B LEU* 3.7 24.9 + - - +
185B PHE* 4.9 2.0 - - - -
186B GLU 3.5 9.9 - - - -
187B PRO* 4.3 1.1 - - - -
188B LYS* 4.2 5.6 - - - -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY* 1.3 71.9 - - - -
31B PHE* 1.3 64.1 + - - +
33B GLN* 3.9 12.0 - - - +
34B GLU* 3.0 45.1 + - - +
113B ILE* 5.3 2.8 - - - +
185B PHE* 3.4 8.0 - - - +
186B GLU* 2.9 47.0 + - - +
188B LYS* 4.1 10.5 - - - +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PRO 3.7 22.7 - - - -
374A TYR* 3.9 23.1 - + + -
375A GLN* 4.2 8.3 - - + -
29B GLY 3.1 1.0 - - - -
30B SER* 1.3 81.3 + - - +
32B ASN* 1.3 78.0 + - - +
34B GLU* 3.2 5.3 + - - +
35B VAL* 3.2 40.4 + - + +
109B VAL* 3.8 39.0 - - + -
169B LEU 3.6 1.1 - - - +
170B ALA* 3.5 23.8 - - + -
171B GLY* 3.5 20.9 - - - -
183B ILE* 4.7 11.9 - - + -
184B SER 5.4 3.1 - - - +
185B PHE* 4.3 8.4 - - + +
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A GLN* 2.8 22.0 + - - +
24B ILE 3.4 18.9 + - - +
25B THR* 4.8 4.3 - - - +
26B HIS 2.8 31.5 + - - +
27B PRO* 4.3 2.9 - - + -
28B GLY 4.8 0.2 - - - +
29B GLY 3.3 7.3 + - - +
31B PHE* 1.3 84.3 - - - +
33B GLN* 1.3 61.7 + - - +
35B VAL* 3.8 8.6 - - - +
36B ALA* 3.3 23.6 + - - +
167B PRO 3.1 23.8 + - - -
168B GLY 3.2 12.3 + - - -
169B LEU 3.6 6.1 + - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PRO* 3.4 37.0 + - + +
29B GLY 3.3 14.6 + - - +
30B SER* 3.9 6.1 - - - +
31B PHE 3.2 0.6 - - - -
32B ASN* 1.3 76.6 - - - +
34B GLU* 1.3 64.6 + - + +
35B VAL 3.6 0.2 + - - -
36B ALA* 3.7 15.2 + - - +
37B PHE* 4.9 1.2 + - - -
188B LYS* 3.5 37.1 + - - +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 3.0 37.5 + - - +
31B PHE* 3.2 4.0 + - - +
33B GLN* 1.3 80.8 - - + +
35B VAL* 1.3 58.8 + - - +
37B PHE* 3.2 25.5 - - - -
105B ALA* 4.9 2.1 - - - +
108B GLN* 4.1 38.6 + - - +
109B VAL* 3.4 31.2 - - + +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PRO* 4.0 20.2 - - + +
372A LEU* 4.4 21.5 - - + +
375A GLN* 5.8 3.6 - - + -
24B ILE 5.8 1.8 - - - +
31B PHE* 3.2 37.6 + - + +
32B ASN* 3.8 13.0 - - - +
34B GLU* 1.3 77.5 - - - +
36B ALA* 1.3 67.9 + - - +
37B PHE* 2.9 9.2 + - - -
38B LEU* 2.9 25.9 + - + +
39B PHE* 4.3 7.0 + - + -
105B ALA* 5.1 3.4 - - + -
109B VAL* 3.9 19.1 - - + -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR 6.1 1.1 - - - +
32B ASN 3.3 19.2 + - - +
33B GLN* 3.7 11.9 - - - +
34B GLU 3.4 1.4 - - - -
35B VAL* 1.3 77.5 - - - +
37B PHE* 1.3 60.1 + - - +
38B LEU 3.1 1.8 + - - -
39B PHE* 3.3 18.9 + - + +
40B PRO* 3.2 17.2 - - - +
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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