Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 1AXS
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 THR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PRO* 5.3 0.5 - - - +
124A GLN* 3.1 42.5 - - - +
125A LEU* 4.8 1.4 - - - -
127A SER* 2.8 18.7 + - - +
128A GLY* 1.3 81.2 + - - +
130A ALA* 1.3 65.1 + - - +
180A THR* 3.6 27.4 - - + -
181A LEU 3.7 3.8 - - - +
182A SER* 4.4 0.2 - - - +
183A LYS* 4.4 4.2 - - - +
143B LYS* 4.6 8.3 - - - -
144B ASP* 5.5 3.1 + - - +
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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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120A PRO* 3.8 20.0 - - + -
124A GLN* 4.2 0.4 - - - -
129A THR* 1.3 76.6 - - - +
131A SER* 1.3 61.6 + - - +
132A VAL 4.1 0.7 - - - -
179A LEU 3.5 1.0 - - - +
180A THR* 3.3 5.2 - - - +
181A LEU* 2.7 46.5 + - + +
182A SER 3.7 11.9 - - - +
183A LYS* 4.6 2.0 - - - -
186A TYR* 3.7 21.3 - - + -
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Residues in contact with SER 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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119A PRO 4.3 1.4 - - - -
120A PRO* 3.6 20.3 - - - +
124A GLN* 3.3 24.5 + - - +
130A ALA* 1.3 73.3 + - - +
132A VAL* 1.3 62.5 + - - +
133A VAL* 3.9 5.9 + - - +
178A THR* 4.0 8.9 - - - +
179A LEU 3.2 3.8 - - - -
180A THR* 3.1 20.4 + - - +
141B LEU* 3.9 15.4 - - - +
143B LYS* 3.5 20.8 + - - -
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Residues in contact with VAL 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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118A PHE 2.9 22.2 - - - +
119A PRO* 4.1 1.1 - - + -
120A PRO* 3.9 16.4 - - + -
131A SER* 1.3 74.9 - - - +
133A VAL* 1.3 60.3 + - - +
148A TRP* 3.6 26.9 - - + -
178A THR* 3.4 2.6 - - - -
179A LEU* 2.7 56.1 + - + +
181A LEU* 4.7 8.5 - - + -
186A TYR* 4.6 9.2 - - + -
192A TYR* 4.6 7.9 - - + -
209A PHE* 3.5 27.6 - - + -
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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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117A ILE* 3.6 5.0 - - - +
118A PHE* 2.9 52.2 + - + +
131A SER 4.3 8.3 - - - +
132A VAL* 1.3 77.4 - - - +
134A CYS* 1.3 71.1 + - - +
135A LEU* 5.5 2.0 - - + -
148A TRP* 3.9 2.5 - - - -
176A SER* 5.0 6.7 - - - -
177A SER 3.5 7.2 - - - +
178A THR* 4.2 13.7 - - + +
124B LEU* 4.0 35.2 - - + -
141B LEU* 4.1 20.9 - - + -
179B SER* 4.6 7.0 - - - +
181B VAL* 6.0 2.2 - - + -
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Residues in contact with CYS 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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115A VAL* 3.8 14.4 - - - -
116A PHE 3.5 10.1 - - - -
117A ILE* 4.7 0.9 - - - +
133A VAL* 1.3 77.6 - - - +
135A LEU* 1.3 64.9 + - - +
136A LEU* 4.2 9.8 - - + +
148A TRP* 3.4 13.9 - - + -
175A LEU 3.9 0.2 - - - +
176A SER* 3.3 7.3 - - - -
177A SER* 2.8 40.6 + - - +
194A CYS* 2.0 51.1 - - - -
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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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114A SER 3.3 2.6 - - - +
115A VAL* 3.1 6.6 - - - -
116A PHE* 2.8 73.4 + - + +
118A PHE* 4.5 10.8 - - + -
133A VAL* 5.5 1.8 - - + -
134A CYS* 1.3 75.3 - - - +
136A LEU* 1.3 79.7 + - - +
137A ASN* 3.8 22.2 - - + +
174A SER* 5.2 1.3 - - - -
175A LEU 3.1 12.8 - - - +
176A SER* 5.0 0.9 - - - -
137B ALA* 4.3 12.3 - - + -
164B HIS* 6.3 0.2 - - + -
166B PHE* 3.9 20.6 - - + -
181B VAL* 4.4 23.8 - - + -
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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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113A PRO* 4.0 10.1 - - + -
114A SER 3.5 5.2 - - - -
115A VAL* 4.2 2.7 - - + -
134A CYS* 4.2 12.3 - - - -
135A LEU* 1.3 79.1 - - - +
137A ASN* 1.3 59.8 + - - +
139A PHE* 3.3 15.8 - - + -
144A ALA* 4.0 18.6 - - + -
146A VAL* 3.5 24.9 - - + -
174A SER* 3.3 4.5 - - - -
175A LEU* 2.8 63.2 + - + +
196A VAL* 3.5 42.4 - - + -
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Residues in contact with ASN 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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113A PRO* 3.6 1.4 - - - +
114A SER* 2.8 41.3 + - - +
116A PHE* 4.2 7.0 - - + -
135A LEU* 3.8 19.4 + - + +
136A LEU* 1.3 74.1 - - - +
138A ASN* 1.3 118.9 + - - +
139A PHE 3.4 2.1 + - - -
174A SER* 3.2 8.8 + - - -
164B HIS* 3.6 15.5 + - - -
181B VAL* 5.4 0.9 - - - +
183B THR* 3.3 31.6 + - - +
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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