Contacts of the strand formed by residues 9 - 14 (chain D) in PDB entry 5EEZ
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 PHE 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ASP* 3.6 41.5 - - + -
9C PHE 5.6 1.6 - - - -
10C VAL* 5.8 0.7 - - + -
48C PHE* 4.3 8.5 - + + -
65C THR* 3.7 28.3 - - - -
66C ARG* 4.1 11.2 - - + -
67C HIS* 3.2 56.3 + + - -
7D SER 4.6 1.8 - - - -
8D ASP* 1.3 82.5 + - - +
10D VAL* 1.3 71.5 + - - +
11D VAL* 3.7 7.4 - - + -
45D ILE* 3.5 22.4 - - + -
46D ALA 3.2 20.2 - - - +
47D GLN* 4.0 9.9 - - + +
48D PHE* 4.7 0.9 - - - +
65D THR* 4.5 4.7 - - - -
66D ARG 4.8 0.3 + - - -
9E PHE* 5.6 1.4 - - - -
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Residues in contact with VAL 10 (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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9D PHE* 1.3 81.0 - - - +
11D VAL* 1.3 61.5 + - - +
12D ILE* 3.6 22.8 - - + +
44D LEU 3.8 0.7 - - - +
45D ILE* 3.4 3.1 - - - +
46D ALA* 2.9 39.4 + - + +
48D PHE* 4.3 12.8 - - + -
55D ILE* 4.0 16.6 - - + -
63D ILE* 4.8 2.0 - - + -
64D GLN 3.6 9.0 - - - +
65D THR* 4.0 13.9 - - + -
9E PHE* 5.7 1.1 - - + -
45E ILE* 4.0 36.1 - - + -
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Residues in contact with VAL 11 (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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65C THR* 4.0 17.7 - - + +
67C HIS* 4.2 2.7 - - + -
70C ILE* 4.0 27.6 - - + -
9D PHE* 3.7 24.7 - - + -
10D VAL* 1.3 77.0 - - - +
12D ILE* 1.3 64.8 + - - +
43D VAL* 4.0 14.8 - - + -
44D LEU 3.6 3.6 - - - +
45D ILE* 4.3 6.7 - - + +
63D ILE* 3.2 10.2 - - - +
64D GLN* 2.9 60.3 + - + +
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Residues in contact with ILE 12 (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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10D VAL* 3.6 27.4 - - + +
11D VAL* 1.3 80.0 - - - +
13D LYS* 1.3 61.1 + - - +
19D VAL* 4.6 0.4 - - + -
21D VAL* 3.8 37.9 - - + -
38D LEU* 3.9 20.1 - - + +
42D GLU 3.9 0.7 - - - +
43D VAL* 3.3 4.5 - - - +
44D LEU* 2.8 46.3 + - + +
46D ALA* 4.9 1.3 - - + -
55D ILE* 4.9 0.7 - - + -
57D VAL* 4.2 17.0 - - + -
61D ALA* 3.8 23.6 - - + -
62D TYR 3.7 2.5 - - - -
63D ILE* 4.2 15.7 - - + -
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Residues in contact with LYS 13 (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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70C ILE* 4.0 22.2 - - + -
71C GLU* 3.0 25.0 + - - +
73C GLU* 2.7 34.7 + - - -
11D VAL* 4.2 0.4 - - - +
12D ILE* 1.3 74.4 - - - +
14D ALA* 1.3 70.2 + - - +
15D LEU* 3.5 21.7 + - + +
41D GLY* 4.4 8.3 - - - +
42D GLU 3.4 5.8 - - - +
43D VAL* 3.8 18.2 - - + -
61D ALA* 3.2 3.7 - - - -
62D TYR* 2.8 46.0 + - + +
51R HIS* 5.9 0.2 + - - -
28S ALA* 3.7 16.0 - - - +
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Residues in contact with ALA 14 (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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12D ILE 4.1 1.2 - - - -
13D LYS* 1.3 73.7 - - - +
15D LEU* 1.3 60.4 + - - +
16D GLU 3.5 15.0 - - - +
19D VAL* 3.8 11.0 - - + -
38D LEU* 3.7 22.8 - - + +
39D ASP 3.4 24.0 - - - +
40D LYS* 4.3 0.2 - - - +
41D GLY* 2.9 26.4 + - - -
42D GLU 2.9 10.1 + - - +
60D LYS 3.9 4.7 - - - -
61D ALA* 4.4 2.2 - - - -
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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