Contacts of the helix formed by residues 134 - 143 (chain K) in PDB entry 4DVQ
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 GLY 134 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107K HIS* 3.6 31.2 - - - +
108K PRO 5.1 1.4 + - - -
109K CYS* 5.1 2.7 - - - -
133K ASN* 1.3 76.2 + - - +
135K PRO* 1.4 77.0 - - - +
137K TRP* 3.0 17.0 + - - +
138K ARG* 3.1 10.6 + - - +
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Residues in contact with PRO 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K HIS* 4.0 26.0 - - + +
133K ASN 4.4 0.9 - - - +
134K GLY* 1.4 80.9 - - - +
136K GLU* 1.3 64.9 + - - +
138K ARG* 3.0 13.1 + - + +
139K PHE* 3.1 19.3 + - - +
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Residues in contact with GLU 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K LYS* 4.6 19.2 + - - +
132K LEU* 3.2 29.2 - - + +
133K ASN 4.3 5.8 + - - +
134K GLY 3.2 1.0 + - - -
135K PRO* 1.3 78.0 - - - +
137K TRP* 1.3 62.3 + - - +
139K PHE* 3.5 18.5 - - + -
140K ASN* 3.0 41.0 + - - +
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Residues in contact with TRP 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K LEU 3.6 22.4 - - - -
107K HIS* 4.4 8.7 - - + -
108K PRO* 3.8 19.7 - - + -
129K VAL* 3.3 27.8 - - + +
132K LEU* 3.7 23.3 - - + +
133K ASN* 3.7 12.7 + - - +
134K GLY 3.0 13.9 + - - +
136K GLU* 1.3 78.2 - - - +
138K ARG* 1.3 87.5 + - + +
140K ASN* 3.4 3.1 - - - +
141K ARG* 2.9 49.2 + - + +
447K MET* 4.0 26.2 - - + -
448K ARG* 3.2 47.5 - - + +
601K HEM 2.9 19.7 + - - -
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Residues in contact with ARG 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K LEU* 3.9 37.7 + - - +
107K HIS* 3.6 27.8 - - - +
134K GLY 3.1 4.8 + - - +
135K PRO* 3.0 10.2 + - + +
137K TRP* 1.3 100.5 - - + +
139K PHE* 1.3 58.3 + - - +
141K ARG* 3.0 6.0 + - - +
142K LEU* 3.0 50.9 + - + +
447K MET* 3.3 32.9 - - + +
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Residues in contact with PHE 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K PRO* 3.1 15.3 + - + +
136K GLU* 3.5 35.0 - - + -
138K ARG* 1.3 75.1 - - - +
140K ASN* 1.3 73.9 + - - +
142K LEU* 4.6 8.3 - - + -
143K ARG* 2.9 58.0 + - - +
299K LEU* 3.5 24.2 - - + -
300K SER 6.1 0.4 - - - -
303K ALA* 6.0 2.7 - - + -
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Residues in contact with ASN 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K CYS 4.8 1.6 - - - +
129K VAL* 4.4 7.6 - - + -
132K LEU* 3.6 23.5 - - + +
136K GLU* 3.0 26.9 + - - +
137K TRP 3.4 8.1 - - - +
139K PHE* 1.3 97.2 - - - +
141K ARG* 1.3 64.3 + - - +
143K ARG* 3.0 13.3 + - - +
144K LEU* 3.4 19.7 + - + +
299K LEU* 4.0 14.5 - - - +
303K ALA* 4.4 8.2 - - - +
307K ASN* 2.7 31.5 + - - +
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Residues in contact with ARG 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K VAL* 4.0 11.2 - - + +
137K TRP* 2.9 37.7 + - + +
138K ARG* 3.0 8.5 + - + +
140K ASN* 1.3 75.6 - - - +
142K LEU* 1.3 63.9 + - + +
144K LEU* 3.1 4.3 + - - +
145K ASN* 2.7 69.0 + - - +
149K LEU* 3.9 8.9 - - - +
447K MET* 3.2 19.7 + - + +
448K ARG 3.2 21.0 + - - -
449K GLN* 2.3 32.7 + - - +
451K LEU* 3.5 20.1 - - - +
601K HEM 3.0 26.0 + - - +
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Residues in contact with LEU 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K ARG* 3.0 55.5 + - + +
139K PHE* 4.3 8.3 - - + +
141K ARG* 1.3 77.2 - - + +
143K ARG* 1.3 62.0 + - - +
144K LEU 3.2 0.2 - - - -
145K ASN* 4.6 8.7 - - - +
146K PRO* 3.0 25.8 - - - +
447K MET* 4.3 22.7 - - + -
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Residues in contact with ARG 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K PHE* 2.9 51.5 + - - +
140K ASN 3.0 7.0 + - - +
142K LEU* 1.3 81.6 - - - +
144K LEU* 1.3 58.7 + - - +
146K PRO* 4.3 5.4 - - - -
147K ASP* 5.1 2.1 - - - +
293K LEU* 3.8 16.5 - - - +
296K LYS* 6.1 0.2 - - - +
298K GLU* 3.3 67.6 + - + +
299K LEU* 4.0 19.7 - - + +
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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