Contacts of the helix formed by residues 130 - 138 (chain A) in PDB entry 4KZX
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.4 18.4 - - - +
78A SER* 3.6 2.4 - - - -
79A SER* 2.7 37.7 + - - -
80A ARG* 4.4 0.8 + - - -
124A VAL* 3.1 26.9 - - + +
125A THR* 3.4 18.9 + - - -
126A ASP 2.7 22.1 + - - +
127A PRO 3.8 4.0 - - - -
129A ALA* 1.3 71.5 - - - +
131A HIS* 1.3 49.4 - - - +
132A GLN* 3.2 1.1 - - - -
133A PRO* 1.6 52.1 - - + +
134A LEU* 3.1 5.9 + - - +
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Residues in contact with HIS 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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127A PRO 3.2 18.3 + - - +
128A ARG* 2.8 24.4 + - - +
129A ALA* 3.4 13.6 + - - -
130A ASP* 1.3 76.3 - - - +
132A GLN* 1.3 84.8 + - + +
133A PRO* 3.0 0.2 - - - -
134A LEU* 3.3 5.5 + - - +
135A THR* 2.7 46.4 + - + +
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Residues in contact with GLN 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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102A ARG* 5.3 4.2 - - - +
103A PHE* 3.7 31.6 + - + +
104A THR 4.6 1.2 + - - -
105A PRO* 4.0 25.8 - - + +
130A ASP 3.2 0.8 - - - -
131A HIS* 1.3 97.9 + - + +
133A PRO* 1.3 63.5 - - + +
135A THR* 2.5 23.0 + - - -
136A GLU* 2.8 21.3 + - - +
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Residues in contact with PRO 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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77A ILE* 4.3 22.2 - - + -
103A PHE* 3.6 40.9 - - + -
108A PHE* 3.8 5.3 - - + -
122A LEU* 4.1 2.0 - - - +
124A VAL* 4.6 4.3 - - + -
130A ASP* 1.6 57.9 - - + +
132A GLN* 1.3 81.5 - - + +
134A LEU* 1.3 64.3 + - + +
136A GLU 3.3 0.2 + - - -
137A ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 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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122A LEU* 6.1 0.4 - - + -
124A VAL* 3.3 31.4 - - + -
127A PRO* 3.1 53.4 - - + +
130A ASP 3.4 8.7 - - - +
131A HIS* 3.6 8.1 - - - +
133A PRO* 1.3 82.9 - - - +
135A THR* 1.3 60.7 + - + +
137A ALA* 3.9 5.5 - - - +
138A SER* 3.5 19.2 + - - -
144A THR* 3.3 25.4 - - + +
153A PRO* 5.1 1.3 - - + -
155A ARG 5.2 5.8 - - - +
156A TYR* 4.0 16.5 - - + +
157A VAL* 3.8 13.9 - - + -
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Residues in contact with THR 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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131A HIS* 2.7 36.9 + - + +
132A GLN* 2.5 24.5 + - - -
134A LEU* 1.3 70.8 - - + +
136A GLU* 1.3 68.5 + - - +
137A ALA 3.1 1.6 - - - -
138A SER* 2.6 25.1 + - - -
139A TYR* 3.5 11.6 + - - +
156A TYR* 5.0 9.2 - - + -
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Residues in contact with GLU 136 (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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103A PHE* 2.0 51.9 - - - -
105A PRO* 3.0 29.6 - - - +
106A GLY* 3.0 10.6 + - - -
107A THR* 2.7 8.7 + - - -
108A PHE* 3.6 26.0 + - + +
109A THR* 4.6 9.1 - - + +
132A GLN* 2.8 21.3 + - - +
133A PRO 3.9 0.4 - - - +
135A THR* 1.3 76.2 + - - +
137A ALA* 1.3 63.2 + - - +
139A TYR* 3.0 24.1 + - - +
140A VAL* 3.9 3.1 + - - +
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Residues in contact with ALA 137 (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 PHE* 3.7 7.6 - - - -
122A LEU* 3.1 34.8 - - + -
133A PRO 2.9 11.7 + - - +
134A LEU* 3.9 6.5 - - - +
135A THR 3.1 0.2 - - - -
136A GLU* 1.3 77.5 - - - +
138A SER* 1.3 57.6 + - - +
139A TYR 3.1 4.2 + - - -
140A VAL* 3.1 13.2 + - - -
141A ASN 3.5 9.4 + - - -
142A LEU* 3.5 27.3 + - + +
144A THR* 4.3 7.4 - - - +
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Residues in contact with SER 138 (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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134A LEU 3.5 3.9 + - - -
135A THR* 2.6 22.2 + - - -
137A ALA* 1.3 79.5 - - - +
139A TYR* 1.3 57.9 + - - +
140A VAL 3.3 2.9 - - - -
141A ASN* 4.8 2.2 - - - +
156A TYR* 3.6 52.6 - - - -
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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