Contacts of the strand formed by residues 116 - 121 (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 ILE 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ILE* 4.5 18.2 - - + -
105D ALA* 3.4 46.7 - - + +
108D LEU* 4.1 13.2 - - + -
109D SER* 3.7 16.6 - - - +
112D LEU* 5.2 4.0 - - + -
114D THR* 3.6 6.0 + - - +
115D THR* 1.3 76.9 - - - +
117D ILE* 1.3 64.0 + - - +
118D LEU* 4.3 13.7 - - + -
133D PHE* 2.8 39.1 + - + -
142D LEU* 3.5 30.5 - - + +
144D LEU* 5.0 4.0 - - + -
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Residues in contact with ILE 117 (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 TRP* 3.9 15.3 - - + -
116D ILE* 1.3 74.6 - - - +
118D LEU* 1.3 65.3 + - - +
119D TRP* 3.3 30.3 - - + +
130D ALA* 4.0 5.4 - - + -
131D ILE 3.3 8.5 - - - +
132D LYS* 3.5 30.5 - - + -
138D VAL* 3.6 36.1 - - + -
141D ALA* 3.8 14.8 - - + -
142D LEU 2.8 11.2 + - - +
143D ASN* 3.7 13.5 - - - +
144D LEU* 2.8 33.4 + - - +
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Residues in contact with LEU 118 (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* 4.1 21.9 - - + +
41D PHE* 4.5 5.2 - - + -
101D GLY 4.2 4.5 - - - -
102D SER* 3.8 23.6 - - - +
105D ALA* 4.3 2.7 - - + -
116D ILE* 4.3 9.4 - - + -
117D ILE* 1.3 74.2 - - - +
119D TRP* 1.3 63.2 + - - +
120D VAL* 3.7 5.5 + - - +
130D ALA* 3.2 4.2 - - - -
131D ILE* 2.8 35.5 + - + +
133D PHE* 3.7 27.6 - - + -
144D LEU* 3.7 34.8 - - + -
146D HIS* 5.3 1.3 - - + -
152D PHE* 3.7 23.1 - - + -
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Residues in contact with TRP 119 (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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4D LEU* 4.3 10.5 - - + -
7D LEU* 4.2 21.1 - - + -
9D TRP* 4.3 12.3 - + - -
19D THR* 5.0 1.3 - - + -
21D PRO* 4.8 4.5 - - + -
23D PHE* 3.9 21.5 - + - -
29D PHE* 3.8 20.7 - + - -
117D ILE* 3.3 33.9 - - + +
118D LEU* 1.3 71.4 - - - +
120D VAL* 1.3 58.5 + - - +
121D VAL* 3.8 4.3 + - + +
127D VAL* 4.1 31.4 - - + -
129D ALA 3.5 7.2 - - - +
130D ALA* 3.5 18.6 - - + -
138D VAL* 4.5 7.2 - - + -
143D ASN* 3.5 21.8 + - - +
144D LEU 2.9 31.3 + - - +
145D MET* 3.7 1.9 - - - -
146D HIS* 2.7 33.1 + - - +
155D LEU* 4.0 15.0 - - + -
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Residues in contact with VAL 120 (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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8C LEU* 4.2 24.7 - - + -
9C THR* 6.0 2.9 - - + -
71C LEU* 6.5 0.9 - - + -
73C LEU* 4.4 19.7 - - + -
118D LEU 4.4 6.3 - - - +
119D TRP* 1.3 73.2 - - - +
121D VAL* 1.3 63.8 + - - +
127D VAL* 3.3 5.7 - - - -
128D THR* 3.0 32.8 + - - +
129D ALA* 2.8 26.8 + - + +
146D HIS* 3.9 15.3 - - + +
149D ARG* 4.6 23.8 - - - +
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Residues in contact with VAL 121 (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* 4.1 2.2 - - + -
119D TRP* 4.0 5.6 - - + +
120D VAL* 1.3 85.5 - - - +
122D ASN* 1.3 77.4 + - - +
125D GLU* 3.7 12.3 - - - +
126D GLN 3.3 17.3 - - - +
127D VAL* 3.9 24.5 - - + -
128D THR* 5.2 0.9 - - - -
145D MET* 3.6 28.5 - - + -
146D HIS 3.0 19.1 + - - +
147D VAL* 4.1 13.8 - - + -
148D GLY 4.6 10.2 + - - -
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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