Contacts of the helix formed by residues 129 - 135 (chain A) in PDB entry 4K8T
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 3.9 24.9 - - + +
11A ILE* 4.8 0.4 - - + -
35A LEU* 3.8 25.1 - - + -
36A ILE 4.7 1.2 + - - -
111A ALA* 3.1 9.8 - - - +
127A THR* 3.9 9.3 + - + -
128A TYR* 1.3 75.7 - - - +
130A GLY* 1.3 67.3 + - - +
132A CYS* 2.8 29.2 + - + +
133A VAL* 4.2 13.9 - - + -
159A ASP* 4.2 7.9 - - + -
160A PRO* 4.1 30.5 - - + -
401A ADN 3.9 23.8 - - - +
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Residues in contact with GLY 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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108A PRO* 3.6 9.2 - - - +
109A PRO 3.3 12.8 - - - -
111A ALA 4.5 0.4 - - - -
128A TYR* 3.3 35.8 - - - -
129A LEU* 1.3 74.9 - - - +
131A ALA* 1.3 58.3 + - - -
132A CYS 3.0 6.1 + - - -
133A VAL* 3.2 26.5 + - - +
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Residues in contact with ALA 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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78A ASN* 2.8 31.3 + - - +
79A VAL* 3.7 8.1 - - - -
80A ALA* 3.6 26.0 - - + +
108A PRO* 3.4 20.4 - - - +
109A PRO 2.7 13.0 + - - +
110A THR* 4.3 2.0 - - - -
111A ALA 4.2 1.6 - - - +
129A LEU 3.2 0.8 + - - -
130A GLY* 1.3 69.0 - - - -
132A CYS* 1.3 62.1 + - - +
133A VAL 3.1 0.9 - - - -
134A GLU* 3.1 22.5 + - - +
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Residues in contact with CYS 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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9A ASN* 3.5 27.6 - - - +
10A ALA 3.3 43.7 - - - -
78A ASN* 4.0 11.9 + - - +
111A ALA* 3.6 7.6 - - - +
129A LEU* 2.8 28.3 + - + +
131A ALA* 1.3 78.1 - - - +
133A VAL* 1.3 60.3 + - - +
134A GLU 3.0 1.9 + - - -
135A LEU* 3.3 18.7 + - - +
160A PRO* 3.8 11.8 - - - +
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Residues in contact with VAL 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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108A PRO* 4.4 11.7 - - + -
129A LEU* 4.2 19.3 - - + -
130A GLY 3.2 19.5 - - - +
132A CYS* 1.3 75.5 - - - +
134A GLU* 1.3 71.0 + - + +
135A LEU 3.4 4.4 + - - +
160A PRO* 3.9 12.3 - - + -
161A PRO* 3.6 34.7 - - + +
162A ARG* 4.9 2.8 + - - +
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Residues in contact with GLU 134 (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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78A ASN* 3.6 3.4 + - - +
104A LYS* 3.4 52.3 - - + +
105A GLY 5.8 0.5 + - - -
107A PHE 4.3 5.2 - - - +
108A PRO* 3.4 29.6 - - + +
131A ALA* 3.1 24.1 + - - +
132A CYS 3.0 1.4 - - - -
133A VAL* 1.3 86.8 - - + +
135A LEU* 1.3 62.2 + - - +
136A GLY 3.4 2.6 + - - -
138A GLU* 3.5 8.0 - - - +
162A ARG* 5.8 1.0 + - - -
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Residues in contact with LEU 135 (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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7A VAL* 4.3 18.8 - - + -
8A GLY 4.3 10.1 - - - +
9A ASN* 5.9 0.9 - - - +
76A PHE* 4.8 4.5 - - + -
77A GLY* 4.3 10.1 - - - +
78A ASN* 4.2 27.7 - - + +
101A THR* 4.5 0.4 - - + -
131A ALA 4.2 1.4 + - - -
132A CYS* 3.3 15.9 + - - +
133A VAL 4.5 2.6 - - - +
134A GLU* 1.3 77.8 - - - +
136A GLY* 1.3 59.9 + - - +
139A ASP* 3.4 33.0 - - + +
157A LEU* 4.1 26.0 - - + -
160A PRO* 5.8 0.5 - - - +
162A ARG* 3.5 6.1 - - - +
163A ALA* 3.4 31.0 + - + +
166A ALA* 5.2 4.9 - - + -
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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