Contacts of the strand formed by residues 99 - 104 (chain D) in PDB entry 2HVY
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 99 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLY 2.9 26.0 + - - -
37D THR* 3.3 27.6 + - - -
40D THR* 3.0 16.1 + - - -
53D ILE 3.1 11.4 - - - -
54D ILE* 4.3 4.9 - - - -
64D VAL* 4.3 2.5 - - - -
67D LEU* 3.5 24.2 - - - +
87D LEU* 4.1 1.1 - - - -
97D ALA* 3.4 1.1 - - - +
98D ALA* 1.3 82.8 - - - +
100D VAL* 1.3 66.2 + - - +
32E U 4.4 0.4 + - - -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 4.0 24.9 - - + -
33D ILE* 4.4 11.4 - - + -
34D ARG 3.4 13.5 - - - +
35D LYS* 4.3 4.0 - - + -
40D THR* 3.4 8.2 - - - +
52D VAL* 3.5 2.8 - - - -
53D ILE* 2.8 38.4 + - + +
87D LEU* 3.8 31.4 - - + -
91D ALA* 4.1 19.7 - - + -
97D ALA* 4.2 7.4 - - + -
99D SER* 1.3 78.3 - - - +
101D ALA* 1.3 69.4 + - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 3.3 5.7 - - - +
34D ARG* 2.7 42.1 + - + +
40D THR* 3.4 28.4 + - + -
43D ALA* 4.0 9.6 - - + -
49D ALA* 3.9 23.1 - - + -
51D LEU 3.4 4.7 - - - +
52D VAL* 4.7 1.1 - - + -
100D VAL* 1.3 75.2 - - - +
102D ILE* 1.3 62.7 + - - +
103D ILE* 4.0 0.9 - - + -
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 4.0 25.4 - - + +
24D VAL* 4.5 2.9 - - + +
27D ALA* 4.2 4.9 - - + -
33D ILE* 3.8 15.9 - - + -
49D ALA* 3.4 1.0 - - - -
50D LYS* 2.7 34.7 + - + -
51D LEU* 2.9 37.3 + - + +
53D ILE* 3.8 24.7 - - + -
100D VAL* 5.2 0.2 - - + -
101D ALA* 1.3 73.3 - - - +
103D ILE* 1.3 59.9 - - - +
104D GLU 3.9 4.0 - - - +
105D PRO* 3.8 39.5 - - + -
112D VAL* 4.1 11.7 - - + -
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LYS* 3.0 33.3 + - + +
33D ILE* 4.5 0.4 - - - -
34D ARG* 3.9 26.7 - - + +
43D ALA* 3.6 32.1 - - + -
48D GLN* 3.6 38.8 - - + +
49D ALA* 3.9 1.6 - - + +
50D LYS* 3.4 28.5 - - - +
101D ALA* 4.7 1.1 - - + -
102D ILE* 1.3 75.9 - - - +
104D GLU* 1.3 81.6 + - + +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA* 3.8 4.2 - - - +
31D GLY* 3.4 8.9 - - - -
32D LYS* 3.0 48.9 + - - +
50D LYS* 6.0 0.7 - - - -
102D ILE* 3.9 2.5 - - - -
103D ILE* 1.3 95.6 - - + +
105D PRO* 1.3 68.8 - - + +
106D GLY 3.3 2.5 - - - +
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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