Contacts of the strand formed by residues 104 - 108 (chain D) in PDB entry 3IKH
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 ALA 104 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PRO* 4.0 15.9 - - + -
22B LYS 3.6 20.0 - - - +
23B LYS* 4.4 0.2 - - - -
25B ALA 3.4 5.4 - - - -
20D ILE* 3.9 22.0 - - + -
94D ILE 3.7 0.7 - - - +
95D ILE* 4.5 0.2 - - - +
96D LEU* 2.8 45.5 + - + +
102D ASP 3.7 0.6 + - - -
103D ASN* 1.3 72.6 - - - +
105D ILE* 1.3 65.5 + - - +
106D ILE* 5.6 0.2 - - - -
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Residues in contact with ILE 105 (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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21B PRO* 4.6 1.2 - - - +
25B ALA 3.0 9.0 + - - +
26B SER* 3.3 20.9 - - - +
27B ILE* 2.8 29.0 + - - +
39D LYS* 5.8 2.2 - - - +
93D SER* 4.3 10.3 - - - +
94D ILE 3.4 9.0 - - - +
95D ILE* 4.3 23.3 - - + -
103D ASN* 4.8 6.7 - - + +
104D ALA* 1.3 82.6 - - - +
106D ILE* 1.3 71.3 + - - +
107D THR* 3.7 19.1 - - - +
228D THR* 5.7 2.2 - - + -
501D GOL 4.3 25.1 - - - -
900D ATP 5.4 8.3 - - - +
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.1 16.2 - - + -
17B ILE* 3.9 29.6 - - + -
21B PRO* 4.0 27.1 - - + -
27B ILE* 3.3 26.2 - - + -
29B GLY* 3.9 11.4 - - - -
95B ILE* 4.3 19.1 - - + -
92D THR 4.0 1.0 - - - +
93D SER* 3.3 1.0 - - - -
94D ILE* 2.9 48.6 + - + +
96D LEU* 5.2 7.6 - - + -
104D ALA 5.6 0.7 - - - +
105D ILE* 1.3 78.4 - - - +
107D THR* 1.3 62.6 + - - +
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Residues in contact with THR 107 (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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15B TRP* 4.9 0.2 - - - -
26B SER* 5.0 2.4 + - - -
27B ILE 2.8 14.1 + - - -
28B HIS* 3.1 18.2 - - + +
29B GLY* 2.8 24.8 + - - -
8D ASN* 3.9 21.8 - - - +
10D THR* 4.2 3.6 - - + -
92D THR 3.6 5.4 - - - +
93D SER* 2.8 26.2 + - - +
105D ILE* 3.7 10.6 - - - +
106D ILE* 1.3 75.6 - - - +
108D THR* 1.3 76.0 + - - +
138D ASN* 4.6 8.6 + - - +
164D PRO* 6.2 0.9 - - - -
501D GOL 4.6 3.0 + - - +
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.6 10.8 - - - -
28B HIS* 5.1 0.2 - - - -
29B GLY 3.3 14.9 + - - -
30B VAL* 4.8 0.9 - - - -
31B LYS* 4.5 14.6 + - + +
8D ASN* 4.9 1.6 + - - +
90D SER 4.5 1.8 - - - +
91D ASP* 3.2 21.9 + - - +
92D THR* 2.8 47.0 + - - +
106D ILE 4.4 0.2 + - - -
107D THR* 1.3 87.0 - - - +
109D THR* 1.3 61.9 + - - +
110D ALA* 3.6 15.5 + - + +
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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