Contacts of the strand formed by residues 125 - 133 (chain A) in PDB entry 1HU9
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 PHE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 6.1 0.2 - - + -
18A LEU* 3.8 24.2 - - + -
19A MET 3.3 13.9 - - - +
20A ARG* 4.5 3.8 - - - -
21A LYS 4.6 1.3 - - - +
53A PHE* 4.0 26.7 - + + -
58A VAL* 3.9 21.5 - - + -
117A ILE* 3.9 23.3 - - + -
119A ASN* 3.4 34.1 - - - -
121A MET* 5.1 0.4 - - - -
123A THR 4.4 3.1 - - - +
124A GLU* 1.3 75.0 - - - +
126A PHE* 1.3 59.9 + - - +
127A LEU* 3.9 16.6 - - + -
148A TRP* 3.4 10.9 - - - -
149A ILE* 2.8 48.2 + - + -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.3 1.2 - - - -
19A MET* 2.8 61.4 + - + +
24A LEU* 4.3 6.3 - - + -
125A PHE* 1.3 72.1 - - - +
127A LEU* 1.3 65.5 + - - +
128A VAL* 3.5 14.3 + - + -
146A ASN* 3.5 54.1 - - + -
147A SER* 3.6 8.5 - - - -
148A TRP* 3.6 47.8 - + + -
261A ASP* 5.0 2.0 - - - -
264A PHE* 5.9 9.9 - + - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.9 22.2 - - + -
17A VAL 3.7 13.7 - - - +
18A LEU* 4.1 4.7 - - + -
60A LEU* 6.4 0.9 - - + -
115A PHE* 4.2 11.0 - - + -
117A ILE* 3.8 24.2 - - + -
125A PHE* 3.6 13.9 + - + -
126A PHE* 1.3 72.3 - - - +
128A VAL* 1.3 59.4 + - - +
129A SER 4.1 6.5 - - - +
130A LEU* 6.1 0.7 - - + -
145A CYS* 3.9 22.2 - - + -
146A ASN* 3.0 19.8 + - - -
147A SER 2.8 21.9 + - - +
149A ILE* 3.6 12.8 - - + -
161A PHE* 3.9 25.4 - - + -
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 2.9 33.0 + - + +
18A LEU* 3.8 13.5 - - - -
19A MET* 3.9 22.4 - - + -
96A GLN* 4.8 10.8 - - + +
126A PHE* 3.9 13.0 - - + +
127A LEU* 1.3 75.0 - - - +
129A SER* 1.3 66.6 + - - +
144A VAL* 4.2 2.1 - - - +
145A CYS* 2.9 25.2 + - - -
146A ASN* 3.1 22.2 + - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR 4.5 0.4 - - - -
16A VAL* 3.7 2.8 - - - -
17A VAL* 3.0 44.2 + - - +
127A LEU* 4.1 7.1 - - - +
128A VAL* 1.3 86.5 - - - +
130A LEU* 1.3 62.9 + - - +
131A THR* 5.1 0.7 + - - -
142A HIS* 3.7 23.0 - - - -
143A PHE 3.2 14.4 - - - -
144A VAL* 4.6 2.7 - - - -
145A CYS* 4.2 7.1 - - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY* 4.6 2.2 - - - -
15A THR 3.5 13.7 - - - +
16A VAL* 3.4 29.4 - - + -
60A LEU* 4.1 12.1 - - + -
62A LEU* 4.8 5.8 - - + -
101A ILE* 4.8 2.2 - - + -
103A PHE* 4.8 1.8 - - + -
115A PHE* 3.7 40.6 - - + -
127A LEU* 6.1 0.7 - - + -
129A SER* 1.3 76.7 - - - +
131A THR* 1.3 70.7 + - - +
132A LEU* 4.1 20.4 - - + -
142A HIS* 3.4 3.5 + - - -
143A PHE* 2.8 53.2 + - + -
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS 3.6 0.7 - - - +
14A GLY* 3.1 6.1 - - - -
15A THR* 3.0 49.6 + - + +
129A SER* 5.1 0.9 + - - -
130A LEU* 1.3 73.2 - - - +
132A LEU* 1.3 73.0 + - - +
133A GLU* 5.2 6.7 - - + +
140A SER* 4.6 11.4 - - - +
141A ILE 3.5 10.3 - - - +
142A HIS* 2.9 29.3 + - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.1 18.8 - - + -
13A LYS 3.3 1.1 - - - -
14A GLY* 3.9 6.5 - - - -
62A LEU* 4.0 18.4 - - + -
103A PHE* 3.8 29.2 - - + -
112A PRO* 4.0 21.5 - - + -
130A LEU* 4.1 11.0 - - + -
131A THR* 1.3 83.0 - - - +
133A GLU* 1.3 61.8 + - - +
134A ASP* 3.4 4.2 + - - +
140A SER* 3.2 10.7 - - - -
141A ILE* 2.9 40.7 + - + +
143A PHE* 3.7 27.8 - - + -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS* 5.3 1.2 - - - -
12A ILE* 4.2 4.3 - - - +
13A LYS* 2.7 60.3 + - + +
15A THR* 4.8 12.6 - - + +
131A THR* 5.2 7.7 - - + +
132A LEU* 1.3 73.6 - - - +
134A ASP* 1.3 68.8 + - - +
140A SER* 4.4 14.6 - - - +
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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