Contacts of the strand formed by residues 142 - 147 (chain D) in PDB entry 4HXD
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 LEU 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLN* 5.4 1.6 - - - +
45D ILE* 4.3 26.2 - - + +
48D LEU* 4.0 36.1 - - + +
49D PHE* 4.4 20.2 - - + +
112D LEU* 5.6 2.9 - - + -
114D THR* 4.1 21.5 - - + -
115D THR 2.8 14.8 + - - +
116D ILE* 3.5 25.7 - - + +
117D ILE 2.8 32.6 + - - +
140D THR 4.9 2.5 - - - +
141D ALA* 1.3 76.0 - - - +
143D ASN* 1.3 58.8 + - - +
144D LEU* 3.8 4.4 + - + +
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Residues in contact with ASN 143 (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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29D PHE* 3.8 12.0 - - + -
48D LEU* 3.3 14.9 - - - +
117D ILE* 3.7 21.8 - - - +
119D TRP* 3.5 20.7 + - - +
138D VAL* 3.4 13.3 + - - +
141D ALA 3.5 9.5 + - - -
142D LEU* 1.3 70.8 - - - +
144D LEU* 1.3 62.6 - - - +
155D LEU* 3.0 46.1 + - + +
157D ILE* 3.2 31.3 - - - +
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Residues in contact with LEU 144 (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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41D PHE* 4.0 18.6 - - + -
44D SER* 3.9 26.9 - - - -
45D ILE* 3.8 33.0 - - + -
48D LEU* 3.9 16.4 - - + -
116D ILE* 5.0 2.5 - - + -
117D ILE 2.8 16.1 + - - +
118D LEU* 3.7 24.7 - - + -
119D TRP* 2.9 34.0 + - - -
142D LEU* 4.4 9.0 - - + +
143D ASN* 1.3 82.8 - - - +
145D MET* 1.3 59.8 + - - +
152D PHE* 4.1 7.2 - - + -
153D ASP 3.6 4.5 - - - +
154D ALA* 5.1 0.4 - - - -
155D LEU* 4.3 1.6 - - - -
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Residues in contact with MET 145 (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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25D VAL* 3.9 29.8 - - - -
31D VAL* 3.9 12.6 - - + -
33D ARG* 3.4 30.5 - - - +
119D TRP* 3.7 2.7 - - + -
121D VAL* 3.6 25.6 - - + -
125D GLU* 4.2 8.7 - - - +
144D LEU* 1.3 74.9 - - - +
146D HIS* 1.3 60.6 + - - +
147D VAL* 3.8 15.6 + - + +
151D HIS 3.4 0.7 - - - +
152D PHE* 3.1 10.7 - - - -
153D ASP* 2.9 56.3 + - + +
155D LEU* 3.9 16.8 - - + -
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Residues in contact with HIS 146 (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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73C LEU* 3.4 33.0 - - + +
74C ARG 3.1 29.1 + - - -
75C GLY* 4.5 0.7 - - - -
118D LEU* 5.3 3.1 - - + -
119D TRP 2.7 23.1 + - - +
120D VAL* 3.9 13.4 - - + +
121D VAL* 3.0 28.1 + - - +
144D LEU 4.2 0.6 + - - -
145D MET* 1.3 71.2 - - - +
147D VAL* 1.3 60.4 + - - +
148D GLY 4.3 0.2 + - - -
149D ARG* 3.5 35.5 + - - +
150D THR 3.9 1.8 - - - -
151D HIS 3.3 7.3 + - - -
152D PHE* 3.1 33.6 - + + -
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Residues in contact with VAL 147 (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 ARG* 5.2 3.1 - - - +
121D VAL* 4.1 17.7 - - + +
122D ASN 5.2 1.8 - - - +
125D GLU* 4.4 6.7 - - - +
145D MET* 3.8 30.5 + - + +
146D HIS* 1.3 77.3 - - - +
148D GLY* 1.3 68.4 + - - +
149D ARG 3.1 1.8 - - - -
150D THR* 3.0 1.0 + - - -
151D HIS* 2.8 60.4 + - + +
153D ASP* 4.9 2.0 - - - +
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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