Contacts of the helix formed by residues 21 - 31 (chain B) in PDB entry 1YYV
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 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 4.0 10.8 - - + -
118A LEU* 4.0 38.4 - - + -
19B GLN 3.5 9.3 - - - +
20B CYS* 1.3 83.8 - - - +
22B SER* 1.3 65.3 + - - +
23B ARG 3.1 0.4 - - - -
24B GLU* 3.0 21.7 + - + +
25B VAL* 3.3 14.4 + - - +
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Residues in contact with SER 22 (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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110A ILE* 3.8 12.6 - - - +
111A GLU* 4.6 4.3 - - - -
114A LEU* 3.9 8.5 - - - +
13B GLY* 4.2 13.9 - - - -
15B LEU* 3.1 31.6 + - - +
20B CYS* 3.1 23.0 - - - +
21B PRO* 1.3 77.9 - - - +
23B ARG* 1.3 58.1 + - - +
25B VAL* 3.1 13.2 - - - +
26B LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 23 (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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32A ARG* 3.1 55.3 - - + +
33A TRP* 3.7 11.8 - - - -
36A LEU* 3.7 15.9 - - - +
56A GLY 3.8 7.7 + - - -
15B LEU* 3.0 45.1 + - + +
16B PHE 3.6 16.0 + - - -
17B ALA 3.6 4.9 + - - +
18B GLU* 3.4 33.4 + - - +
20B CYS 3.0 14.0 + - - +
22B SER* 1.3 81.2 + - - +
24B GLU* 1.3 55.9 + - - +
26B LEU* 3.5 8.0 - - + +
27B LYS* 2.9 28.6 + - - +
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Residues in contact with GLU 24 (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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121A ARG* 3.5 29.8 + - - -
20B CYS 4.3 0.2 + - - -
21B PRO* 3.0 15.6 + - + +
23B ARG* 1.3 73.4 - - - +
25B VAL* 1.3 68.7 + - + +
27B LYS* 3.2 15.3 + - + +
28B HIS* 3.1 46.9 + - - +
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Residues in contact with VAL 25 (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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110A ILE* 2.8 41.3 - - + -
114A LEU* 4.1 11.0 - - + -
117A VAL* 3.7 30.5 - - + -
118A LEU* 5.3 3.8 - - + -
121A ARG* 5.4 2.9 - - - -
21B PRO 3.6 11.0 - - - +
22B SER* 3.1 10.1 - - - +
24B GLU* 1.3 76.4 - - + +
26B LEU* 1.3 63.2 + - - +
28B HIS* 3.2 11.3 + - + +
29B VAL* 3.1 27.7 + - - +
73B ASP* 4.4 12.1 - - - +
75B PHE* 5.2 6.7 - - + -
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Residues in contact with LEU 26 (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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30A THR* 4.4 7.0 - - + +
32A ARG* 5.1 11.0 - - + -
35A VAL* 3.9 36.8 - - + -
103A VAL* 5.9 1.3 - - + +
106A LEU* 4.6 11.2 - - + -
107A ALA* 5.0 4.5 - - - -
110A ILE* 3.8 23.8 - - + -
15B LEU* 4.1 24.9 - - + -
22B SER 2.9 20.0 + - - +
23B ARG* 3.5 8.5 - - + +
25B VAL* 1.3 76.9 - - - +
27B LYS* 1.3 59.3 + - - +
29B VAL* 3.3 1.1 + - - +
30B THR* 2.9 46.9 + - + +
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Residues in contact with LYS 27 (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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23B ARG 2.9 14.3 + - - +
24B GLU* 3.3 17.9 - - + +
26B LEU* 1.3 76.4 - - - +
28B HIS* 1.3 67.1 + - + +
30B THR* 3.9 5.5 - - - +
31B SER* 3.0 34.1 + - - -
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Residues in contact with HIS 28 (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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121A ARG* 3.9 17.7 - - - -
24B GLU* 3.1 46.7 + - + +
25B VAL* 3.2 8.9 + - + +
27B LYS* 1.3 91.2 - - + +
29B VAL* 1.3 60.3 + - - +
30B THR 3.2 0.8 + - - -
31B SER* 3.7 5.5 + - - -
34B GLY* 3.7 14.2 - - - -
66B SER* 5.6 1.2 - - - -
69B ALA* 3.9 24.5 - - + +
70B LEU* 3.5 19.8 - - + +
73B ASP* 2.9 27.6 + - - +
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Residues in contact with VAL 29 (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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106A LEU* 4.1 7.4 - - + -
110A ILE* 3.7 27.4 - - + -
25B VAL 3.1 14.9 + - - +
26B LEU* 3.9 4.3 - - - +
28B HIS* 1.3 78.2 - - + +
30B THR* 1.3 63.2 + - - +
31B SER 3.6 0.2 - - - -
34B GLY 4.0 0.9 - - - -
35B VAL* 3.4 22.8 + - - +
38B LEU* 3.8 17.6 - - + +
70B LEU* 4.1 4.7 - - + -
75B PHE* 3.5 35.7 - - + -
99B VAL* 4.1 9.6 - - + -
103B VAL* 3.6 24.1 - - + +
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Residues in contact with THR 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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26A LEU* 4.3 6.2 - - - +
30A THR* 3.4 59.5 + - - +
106A LEU* 3.7 18.9 - - - +
26B LEU* 2.9 29.6 + - + +
27B LYS* 4.2 5.6 - - - +
29B VAL* 1.3 81.7 + - - +
31B SER* 1.3 66.0 + - - +
32B ARG 3.7 0.5 + - - -
35B VAL* 3.6 11.8 - - - +
103B VAL* 5.4 0.3 - - - +
106B LEU* 4.8 1.4 - - - +
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Residues in contact with SER 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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27B LYS* 3.0 19.1 + - - -
28B HIS* 3.7 6.1 + - - -
29B VAL 3.6 0.2 - - - -
30B THR* 1.3 81.9 - - - +
32B ARG* 1.3 57.0 + - - +
33B TRP* 3.8 4.0 + - - +
34B GLY* 3.1 20.4 + - - -
35B VAL* 2.8 31.8 + - - +
66B SER* 4.4 8.5 + - - -
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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