Contacts of the helix formed by residues 120 - 130 (chain A) in PDB entry 5HLB
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ILE* 1.3 73.7 - - - +
121A LYS* 1.4 58.5 + - - +
122A ASN* 3.9 7.0 + - - +
123A GLU* 3.2 24.1 + - - +
124A MET* 3.0 29.5 + - - +
175A PHE* 3.6 7.9 - - - -
177A GLY* 5.6 3.6 - - - -
178A ASP* 3.4 35.9 + - - -
751A THR* 5.1 3.8 + - - +
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Residues in contact with LYS 121 (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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120A SER* 1.4 72.3 - - - +
122A ASN* 1.3 70.3 + - - +
124A MET 3.5 0.2 + - - -
125A VAL* 3.1 33.3 + - - +
147A VAL* 3.6 16.9 - - + +
148A GLN 2.8 28.8 + - - +
149A ALA* 2.9 24.5 + - - +
150A ASN* 4.5 1.6 - - - -
151A SER 3.8 15.5 - - - +
152A ILE* 3.4 17.9 - - + +
175A PHE* 3.5 36.9 - - + +
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Residues in contact with ASN 122 (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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120A SER* 3.3 7.7 + - - +
121A LYS* 1.3 86.2 - - - +
123A GLU* 1.3 63.6 + - - +
125A VAL* 3.6 9.3 + - - +
126A LYS* 3.4 26.0 + - - +
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Residues in contact with GLU 123 (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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118A THR 4.0 6.5 - - - +
119A ILE* 3.6 25.8 - - + +
120A SER* 3.2 32.4 + - - +
122A ASN* 1.3 76.3 - - - +
124A MET* 1.4 57.5 + - - +
126A LYS* 3.5 12.7 + - - +
127A LEU* 3.0 26.7 + - - +
178A ASP* 4.5 2.8 - - - +
445A VAL* 5.7 3.9 - - + +
751A THR* 3.6 51.5 + - - +
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Residues in contact with MET 124 (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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113A LEU* 3.5 37.5 - - + -
119A ILE* 3.6 28.4 - - + +
120A SER 3.0 14.7 + - - +
121A LYS 3.7 2.7 - - - +
123A GLU* 1.4 72.8 - - - +
125A VAL* 1.4 54.7 + - - +
127A LEU* 3.4 18.5 - - - +
128A LEU* 2.7 45.6 + - + +
152A ILE* 3.8 14.4 - - + -
173A LEU* 3.7 25.8 - - + -
175A PHE* 3.7 16.2 - - + -
180A LEU* 3.7 7.9 - - + -
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Residues in contact with VAL 125 (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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121A LYS* 3.1 21.9 + - + +
122A ASN* 3.8 9.4 - - - +
123A GLU 3.4 0.4 - - - -
124A MET* 1.4 72.7 - - - +
126A LYS* 1.3 52.9 + - + +
128A LEU* 3.2 5.0 + - - +
129A GLU* 2.8 50.0 + - - +
135A GLN* 4.6 7.6 - - - +
145A PHE* 3.6 25.3 - - + -
147A VAL* 3.8 23.8 - - + -
152A ILE* 3.7 14.1 - - + -
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Residues in contact with LYS 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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122A ASN 3.4 12.5 + - - +
123A GLU* 3.6 13.0 - - - +
124A MET 3.4 0.2 - - - -
125A VAL* 1.3 77.9 - - + +
127A LEU* 1.4 56.4 + - - +
129A GLU* 3.8 14.7 - - - +
130A ALA* 3.0 31.1 + - - +
445A VAL* 3.7 31.8 + - + +
449A ALA* 5.9 0.2 - - - +
749A ASN 3.5 23.3 + - - -
750A GLN* 4.3 12.7 - - - +
751A THR* 5.2 6.1 - - - +
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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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109A ARG* 6.5 0.2 - - - -
111A VAL* 4.3 22.2 - - + -
113A LEU* 4.3 8.3 - - + -
119A ILE* 3.9 17.7 - - + -
123A GLU 3.0 16.0 + - - +
124A MET* 3.2 32.7 + - - +
126A LYS* 1.4 73.9 - - - +
128A LEU* 1.4 57.3 + - - +
130A ALA* 3.4 4.3 + - - +
131A THR* 2.8 34.1 + - - +
197A LEU* 3.9 26.0 - - + -
443A ASP* 5.9 0.7 - - - +
445A VAL* 4.1 25.7 - - + +
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Residues in contact with LEU 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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113A LEU* 6.0 0.2 - - + -
124A MET* 2.7 37.5 + - + +
125A VAL 3.6 4.0 - - - +
127A LEU* 1.4 71.1 - - - +
129A GLU* 1.4 59.2 + - - +
131A THR* 3.0 19.6 + - - -
133A TYR* 3.1 42.4 + - + +
145A PHE* 3.9 24.0 - - + -
152A ILE* 3.8 29.8 - - + -
154A MET* 3.7 35.7 - - + -
197A LEU* 4.3 16.2 - - + -
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Residues in contact with GLU 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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125A VAL* 2.8 37.4 + - - +
126A LYS* 3.8 17.0 - - - +
128A LEU* 1.4 71.1 - - - +
130A ALA* 1.4 60.0 + - - +
131A THR 3.2 1.0 + - - -
132A GLN* 3.3 17.3 + - - +
133A TYR 3.6 13.6 + - - +
135A GLN* 4.6 11.5 - - - +
145A PHE* 3.8 15.9 - - + -
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Residues in contact with ALA 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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126A LYS 3.0 19.6 + - - +
127A LEU 3.5 5.8 - - - +
128A LEU 3.3 0.2 - - - -
129A GLU* 1.4 74.7 - - - +
131A THR* 1.4 58.0 + - - +
132A GLN* 3.5 1.8 - - - -
200A ARG* 3.0 26.7 + - - +
444A SER* 3.4 25.2 + - - -
445A VAL* 4.1 16.6 - - + +
448A ASP* 4.5 11.0 - - - +
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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