Contacts of the strand formed by residues 135 - 143 (chain B) 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 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 4.1 9.8 - - - -
129B LYS* 3.5 18.5 - - - +
134B GLY* 1.3 81.1 + - - +
136B ALA* 1.3 63.5 + - - +
183B THR* 5.3 9.1 - - - +
184B VAL 3.6 7.0 - - - +
185B PRO* 3.4 31.2 - - + -
186B SER* 3.5 7.6 - - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 4.3 1.8 - - - -
126B PRO* 4.8 4.9 - - + -
127B SER 4.1 10.5 - - - +
128B SER* 5.7 0.2 - - - -
129B LYS* 3.8 20.2 - - + +
135B THR* 1.3 75.9 - - - +
137B ALA* 1.3 62.9 + - - +
183B THR* 3.6 3.8 - - - -
184B VAL* 3.0 36.1 + - - +
186B SER* 3.6 19.6 - - - +
189B LEU* 4.7 15.3 - - + -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.7 32.8 - - + -
118A PHE* 3.5 14.1 - - + -
135A LEU* 4.3 9.9 - - + -
126B PRO* 3.2 22.2 - - - +
127B SER 4.4 0.9 + - - -
129B LYS* 5.5 0.2 - - - +
136B ALA* 1.3 74.4 - - - +
138B LEU* 1.3 62.3 + - - +
181B VAL* 5.6 2.0 - - + -
182B VAL 3.4 7.2 - - - +
183B THR* 3.4 23.6 - - + -
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Residues in contact with LEU 138 (chain B).
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* 4.4 3.6 - - - -
124B LEU* 3.4 6.7 - - - -
126B PRO* 3.5 30.1 - - + -
137B ALA* 1.3 75.9 - - - +
139B GLY* 1.3 56.7 + - - +
154B TRP* 4.5 3.4 - - + -
181B VAL* 4.2 4.0 - - - -
182B VAL* 2.6 68.3 + - + +
184B VAL* 3.4 29.4 - - + -
189B LEU* 5.8 0.4 - - + -
194B TYR* 4.1 28.5 - - + -
211B VAL* 3.9 32.8 - - + +
212B GLU 6.0 0.2 - - - -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 2.9 37.6 + - - +
138B LEU* 1.3 79.1 - - - +
140B CYS* 1.3 60.4 + - - -
154B TRP* 3.6 11.7 - - - -
180B SER 2.9 13.7 - - - -
181B VAL* 3.8 2.2 - - - -
211B VAL* 3.1 16.3 - - - +
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 3.7 15.3 - - + -
122B PHE 3.4 4.7 - - - +
124B LEU* 3.7 6.3 - - - +
139B GLY* 1.3 72.3 - - - -
141B LEU* 1.3 60.8 + - - +
142B VAL* 3.8 4.4 + - + +
154B TRP* 4.2 2.7 - - + -
179B SER* 3.7 3.6 - - - -
180B SER* 2.7 36.1 + - - +
196B CYS* 2.0 53.6 - - + -
198B VAL* 5.0 3.8 - - + -
209B LYS* 3.8 5.2 - - - -
211B VAL* 3.3 24.5 - - - -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 4.3 2.9 - - - +
131A SER* 3.9 27.4 - - - +
133A VAL* 4.1 18.2 - - + -
178A THR* 4.8 10.1 - - + +
120B SER 3.4 3.1 - - - +
121B VAL* 3.1 4.3 - - - -
122B PHE* 2.8 64.8 + - + +
124B LEU* 3.9 15.1 - - + +
140B CYS* 1.3 71.6 - - - +
142B VAL* 1.3 63.5 + - - +
143B LYS* 3.6 13.9 + - + -
177B SER* 5.9 2.9 - - - -
178B LEU 4.0 7.9 - - - +
179B SER* 3.3 22.4 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PRO* 3.5 15.0 - - + -
120B SER 3.7 3.4 - - - -
121B VAL* 4.4 5.6 - - + -
140B CYS* 3.8 5.5 + - + +
141B LEU* 1.3 72.8 - - - +
143B LYS* 1.3 57.8 + - - +
145B TYR* 3.4 31.4 - - + -
150B VAL* 4.6 5.4 - - + -
152B VAL* 4.7 4.7 - - + -
177B SER* 3.0 22.2 - - - -
178B LEU* 3.1 30.2 + - + +
180B SER* 6.3 0.4 - - - -
198B VAL* 3.4 42.2 - - + -
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 4.0 15.7 - - - +
129A THR* 4.6 11.4 - - - -
131A SER* 3.5 26.7 + - - +
160A GLN* 5.6 1.4 + - - -
178A THR* 5.1 5.3 - - - +
180A THR* 3.7 14.7 + - - +
119B PRO* 3.6 1.2 - - - +
120B SER* 2.8 46.5 + - - +
122B PHE* 4.1 16.2 - - + -
141B LEU* 3.6 13.2 + - + -
142B VAL* 1.3 74.6 - - - +
144B ASP* 1.3 88.3 + - - +
145B TYR* 3.8 1.6 - - - -
171B GLN* 2.6 32.0 + - - -
176B TYR 4.0 0.2 - - - -
177B SER* 3.7 9.9 + - - -
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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