Contacts of the strand formed by residues 126 - 133 (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 GLN 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D THR* 3.5 30.1 - - + +
23D PHE 3.6 18.6 - - - +
24D CYS* 4.6 7.0 - - - +
25D VAL* 4.2 0.4 - - - -
121D VAL* 3.3 9.0 - - - +
122D ASN* 2.6 51.5 + - + +
124D THR* 3.8 16.8 - - - +
125D GLU* 1.3 77.0 - - - +
127D VAL* 1.3 66.0 + - - +
128D THR* 3.5 2.7 + - + +
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Residues in contact with VAL 127 (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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21D PRO* 4.4 7.4 - - + -
22D THR* 3.2 19.6 - - - +
23D PHE* 3.0 58.4 + - + +
25D VAL* 3.7 26.0 - - + -
29D PHE* 5.6 2.5 - - + -
119D TRP* 4.1 24.9 - - + -
120D VAL 3.3 11.0 - - - +
121D VAL* 3.9 9.6 - - + -
126D GLN* 1.3 71.9 - - - +
128D THR* 1.3 63.4 + - - +
129D ALA 4.8 2.2 - - - +
155D LEU* 5.9 0.9 - - + -
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Residues in contact with THR 128 (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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9C THR* 3.4 29.4 - - - +
20D ASN* 3.8 5.2 - - - +
21D PRO 3.2 15.2 - - - +
22D THR* 4.0 20.4 + - + +
120D VAL* 3.0 15.8 + - - +
121D VAL 5.2 0.2 - - - -
122D ASN* 3.0 33.7 + - - +
126D GLN* 3.5 3.5 + - + +
127D VAL* 1.3 78.9 - - - +
129D ALA* 1.3 68.1 + - - +
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Residues in contact with ALA 129 (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* 3.2 39.0 - - + +
9C THR* 4.1 6.3 - - + -
19D THR 3.4 9.4 - - - -
20D ASN* 4.0 3.6 - - - +
21D PRO* 3.9 3.3 + - - +
119D TRP* 3.5 5.2 - - - +
120D VAL* 2.8 42.1 + - + +
127D VAL* 3.8 2.9 - - - +
128D THR* 1.3 80.5 + - - +
130D ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 130 (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* 4.4 2.3 - - - +
9D TRP* 3.7 18.7 - - + -
18D ILE* 3.5 5.5 - - - +
19D THR* 3.0 31.9 + - + +
21D PRO* 5.9 0.2 - - + -
117D ILE* 4.0 2.7 - - + -
118D LEU 3.2 13.5 - - - +
119D TRP* 3.5 31.4 - - + -
120D VAL* 4.5 1.6 - - - +
129D ALA* 1.3 77.6 - - - +
131D ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 131 (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* 4.0 21.3 - - + -
42C ARG* 5.5 2.7 - - - +
70C VAL* 3.7 25.6 - - + -
71C LEU 4.4 1.6 - - - +
73C LEU* 3.5 31.2 - - + -
9D TRP* 4.0 2.5 - - - -
16D GLN* 5.0 4.3 - - + -
17D TYR 3.1 18.2 - - - +
18D ILE* 4.1 7.2 - - + -
102D SER* 4.9 2.9 - - - -
116D ILE 3.8 0.9 - - - +
117D ILE* 3.3 4.5 - - - -
118D LEU* 2.8 33.6 + - + +
130D ALA* 1.3 78.2 - - - +
132D LYS* 1.3 66.1 + - - +
133D PHE* 3.9 32.5 - - + -
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Residues in contact with LYS 132 (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* 3.6 46.8 - - + +
15D GLU 4.0 0.3 - - - +
16D GLN* 3.5 3.8 - - - -
17D TYR* 2.7 67.2 + - + +
115D THR* 3.8 4.9 - - - +
116D ILE 3.7 2.0 - - - -
117D ILE* 3.5 22.9 - - + -
131D ILE* 1.3 74.9 - - - +
133D PHE* 1.3 62.5 + - - +
134D GLY 2.8 26.0 - - - +
135D PRO* 3.0 21.0 + - - +
136D GLY 3.3 17.6 + - - +
137D ARG* 5.5 0.4 - - - +
138D VAL* 5.1 1.6 - - + -
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Residues in contact with PHE 133 (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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42C ARG* 5.2 2.5 - - - -
15D GLU 3.9 2.2 - - - -
16D GLN* 3.6 30.1 - - + -
78D GLU* 4.9 2.7 - - - -
102D SER* 3.3 34.8 - - - -
105D ALA* 3.6 24.5 - - + +
106D SER* 3.6 20.9 - - - -
109D SER* 3.3 22.8 + - - -
115D THR* 3.1 7.3 + - - -
116D ILE 2.8 49.2 + - - +
118D LEU* 3.7 20.0 - - + -
131D ILE* 3.9 26.7 - - + -
132D LYS* 1.3 73.6 - - - +
134D GLY* 1.3 59.8 - - - +
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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