Contacts of the helix formed by residues 134 - 140 (chain A) in PDB entry 3UJK
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 ARG 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A CYS 5.0 1.8 + - - -
111A PRO* 3.9 13.7 - - - +
133A PRO* 1.3 87.5 - - - +
135A PHE* 1.3 64.3 + - - +
136A LEU* 3.2 2.9 - - - -
137A GLN* 3.1 41.7 + - + +
138A VAL* 3.3 9.7 + - + +
154A PRO 5.8 0.2 - - - -
157A SER* 4.6 17.5 - - - +
158A ALA 3.2 11.1 + - - +
159A HIS* 3.1 24.7 + - + +
378A GLU* 3.1 37.4 + - - +
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Residues in contact with PHE 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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132A ILE* 3.5 27.6 - - + +
133A PRO 3.1 4.9 + - - -
134A ARG* 1.3 75.7 - - - +
136A LEU* 1.3 87.0 + - + +
138A VAL* 3.2 2.3 + - - +
139A SER* 2.7 35.4 + - - +
158A ALA* 3.2 35.8 + - + -
160A PHE* 3.6 23.1 - + + -
181A HIS* 3.8 25.6 - - + -
184A LEU* 3.7 29.2 - - + -
185A THR* 3.6 11.2 - - - -
205A TRP* 3.8 9.6 - + - -
238A VAL* 4.0 12.1 - - + -
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Residues in contact with LEU 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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134A ARG 3.1 1.2 + - - -
135A PHE* 1.3 100.9 - - + +
137A GLN* 1.3 60.4 + - + +
139A SER* 3.5 1.7 + - - -
140A SER* 3.0 29.1 + - - -
152A PHE* 3.4 44.2 - - + -
153A ASN 5.1 6.7 - - - +
154A PRO* 5.7 2.7 - - + -
158A ALA* 4.6 11.4 + - + +
185A THR* 3.5 36.7 - - + +
188A ILE* 4.2 12.6 - - + -
205A TRP* 4.0 23.3 - - + -
240A PHE* 5.9 0.7 - - + -
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Residues in contact with GLN 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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134A ARG* 3.1 37.7 + - + +
136A LEU* 1.3 76.9 - - + +
138A VAL* 1.3 66.5 + - + +
139A SER 3.2 0.4 - - - -
140A SER 3.1 19.9 + - - +
141A SER* 4.2 2.9 + - - -
152A PHE* 4.8 4.0 - - + -
154A PRO* 3.8 38.8 - - + +
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Residues in contact with VAL 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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132A ILE* 3.8 22.4 - - + -
133A PRO 3.6 15.7 - - - +
134A ARG* 3.6 14.1 - - + +
135A PHE 3.2 7.3 + - - +
137A GLN* 1.3 80.8 - - + +
139A SER* 1.3 63.3 + - - +
140A SER* 3.4 0.9 + - - -
181A HIS* 5.7 2.9 - - + +
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Residues in contact with SER 139 (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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135A PHE* 2.7 20.3 + - - -
136A LEU 4.0 1.3 - - - -
137A GLN 3.2 0.4 - - - -
138A VAL* 1.3 76.6 - - - +
140A SER* 1.3 62.0 + - - +
181A HIS* 3.6 24.9 + - - -
182A LEU* 3.7 24.4 - - - +
185A THR* 3.2 32.1 + - - +
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Residues in contact with SER 140 (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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136A LEU 3.0 15.9 + - - +
137A GLN* 3.1 16.8 - - - +
138A VAL 3.3 2.1 - - - -
139A SER* 1.3 81.0 - - - +
141A SER* 1.3 66.8 + - - +
150A ASN* 5.1 2.5 + - - -
152A PHE* 3.4 22.4 - - - -
185A THR* 4.0 9.4 - - - +
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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