Contacts of the strand formed by residues 137 - 142 (chain D) in PDB entry 1XSK
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 ASN 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D HIS* 2.7 26.0 + - - +
19D PRO* 3.3 26.6 - - - +
55D LEU* 5.4 2.4 - - - +
69D ILE* 4.7 12.7 - - + +
118D TRP* 4.9 8.2 + - - +
120D LEU* 4.2 12.1 - - - +
132D SER* 3.2 14.3 + - - -
133D GLN 5.0 0.4 - - - +
135D LYS 3.3 2.5 + - - -
136D ASN* 1.3 78.5 + - - +
138D GLY* 1.3 60.5 + - - +
151D PHE* 3.0 25.5 - - - +
152D GLU* 3.0 31.1 + - + +
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Residues in contact with GLY 138 (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 ILE 3.4 9.4 - - - -
19D PRO* 4.0 4.7 - - - -
53D PHE* 3.9 16.8 - - - -
69D ILE* 4.4 5.9 - - - +
137D ASN* 1.3 79.7 + - - +
139D TYR* 1.3 60.6 + - - -
150D MET* 3.4 9.7 - - - +
151D PHE* 3.0 33.6 + - - +
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Residues in contact with TYR 139 (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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15D ASN 3.8 1.7 - - - +
16D LEU* 3.5 9.6 - - - +
17D ILE* 2.8 54.7 + - + +
53D PHE* 3.8 9.8 - - + -
71D HIS* 3.2 36.5 + + + -
72D PHE* 4.7 3.6 - - - -
138D GLY* 1.3 74.0 - - - -
140D VAL* 1.3 64.1 + - - +
141D GLN* 4.5 23.3 + - + -
148D ASN* 3.3 34.1 + - + +
149D TYR 3.4 12.6 - - - -
150D MET* 3.6 15.3 - - - -
151D PHE* 4.5 0.4 - - - -
234D SER 4.3 4.9 - - - -
235D GLU* 2.5 34.0 + - - -
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Residues in contact with VAL 140 (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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1D MET* 4.4 4.3 - - + -
3D ILE* 4.1 12.8 - - + -
14D LEU* 4.1 31.9 - - + -
15D ASN 3.8 1.8 - - - -
16D LEU* 3.6 20.9 - - + -
139D TYR* 1.3 76.7 - - - +
141D GLN* 1.3 62.8 + - - +
142D ASP 3.8 0.2 + - - -
148D ASN* 3.2 6.8 - - - +
149D TYR* 2.5 67.1 + - + +
151D PHE* 3.4 31.4 - - + -
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Residues in contact with GLN 141 (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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13D GLY 3.6 0.2 - - - +
14D LEU* 3.7 0.2 - - - -
15D ASN* 3.0 67.0 + - + +
139D TYR* 4.5 16.4 - - + -
140D VAL* 1.3 74.4 - - - +
142D ASP* 1.3 62.9 + - - +
143D THR* 3.2 10.3 + - - +
148D ASN* 3.5 20.4 + - - +
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Residues in contact with ASP 142 (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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1D MET* 5.6 1.7 - - - +
14D LEU* 3.4 22.7 - - + +
140D VAL 3.8 2.0 - - - -
141D GLN* 1.3 70.8 - - - +
143D THR* 1.3 58.2 + - - +
144D ASN* 3.0 31.9 + - - +
145D ASN* 2.9 32.1 + - - +
146D GLN* 3.0 28.9 + - - -
147D ARG 2.8 21.1 + - - +
148D ASN* 5.3 0.2 - - - +
149D TYR* 3.9 16.5 + - + -
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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