Contacts of the strand formed by residues 16 - 21 (chain D) in PDB entry 5IXM
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 LYS 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.0 10.4 - - - +
15D GLN* 1.3 85.7 - - + +
17D LEU* 1.3 62.1 + - - +
42D THR* 3.3 21.5 - - + +
44D VAL* 4.7 10.5 - - + -
52D ILE* 3.5 27.7 - - + +
53D PRO* 4.1 5.4 - - - +
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Residues in contact with LEU 17 (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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14D LEU* 3.4 33.0 - - + -
16D LYS* 1.3 75.2 - - - +
18D LEU* 1.3 83.5 + - - +
19D LEU* 4.4 5.8 - - + +
36D LEU* 4.3 26.2 - - + -
41D VAL* 3.7 17.5 - - + -
42D THR 2.9 9.6 + - - +
43D ILE* 3.5 6.0 - - + -
44D VAL* 2.9 26.4 + - - +
52D ILE* 3.8 4.3 - - - -
53D PRO 3.4 13.9 - - - +
54D THR 5.4 0.7 - - - -
55D LEU* 4.3 18.6 - - + +
139D LEU* 4.6 11.9 - - + -
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Residues in contact with LEU 18 (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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17D LEU* 1.3 82.0 - - - +
19D LEU* 1.3 62.4 + - - +
20D GLU* 4.2 1.3 - - + +
44D VAL* 3.4 38.4 - - + +
45D ASP 4.3 0.9 - - - -
46D ASP 3.3 31.2 - - - +
47D ALA* 4.6 2.0 - - - -
48D MET* 4.1 14.6 - - - +
49D ARG* 4.7 6.7 - - + +
52D ILE* 4.2 13.9 - - + +
53D PRO 3.0 9.1 + - - +
54D THR* 3.7 30.1 - - + -
55D LEU 2.9 23.8 + - - -
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Residues in contact with LEU 19 (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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17D LEU* 4.4 2.2 - - + -
18D LEU* 1.3 76.8 - - - +
20D GLU* 1.3 60.2 + - - +
21D SER* 4.3 3.7 + - - -
29D ALA* 5.0 2.9 - - + +
32D ILE* 4.4 7.2 - - + -
33D ARG* 3.7 53.0 + - + +
36D LEU* 4.1 17.0 - - + -
43D ILE* 3.8 18.4 - - + -
44D VAL 4.1 6.5 + - - -
55D LEU* 3.5 31.6 - - + +
57D ILE* 3.8 23.1 - - + -
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Residues in contact with GLU 20 (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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18D LEU* 6.3 1.1 - - + -
19D LEU* 1.3 74.1 - - - +
21D SER* 1.3 64.0 + - - +
54D THR* 4.3 17.0 + - - +
55D LEU 2.9 10.4 + - - +
56D ARG* 2.7 58.7 + - + +
57D ILE* 2.9 26.9 + - - +
89D LEU* 4.7 0.5 - - - +
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Residues in contact with SER 21 (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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97C GLN* 5.5 0.9 + - - -
19D LEU* 4.3 4.9 + - - -
20D GLU* 1.3 78.5 - - - +
22D SER* 1.3 66.9 + - - +
23D ASP* 3.0 26.3 + - - +
24D PRO* 3.5 23.0 - - - +
29D ALA* 4.6 9.5 - - - +
33D ARG* 6.1 0.9 - - - -
56D ARG* 5.8 0.2 - - - -
57D ILE* 3.7 26.5 - - - +
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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