Contacts of the strand formed by residues 124 - 131 (chain B) in PDB entry 3IML
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 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.7 15.3 - - - -
171A GLN* 2.8 21.0 + - - +
123B GLN* 1.3 75.0 - - - +
125B LEU* 1.3 58.7 - - - -
126B MET* 3.6 14.7 - - - +
275B ASP* 5.3 1.3 - - - -
303B SER* 3.1 3.5 - - - -
304B TYR* 2.9 28.3 + - - +
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Residues in contact with LEU 125 (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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8A THR* 3.5 18.8 - - + +
9A SER* 3.9 5.4 - - - -
10A GLU* 3.7 46.6 + - + +
171A GLN* 4.5 2.0 - - - +
251A ILE* 4.6 2.2 - - + -
256A GLY 3.5 21.3 - - - +
257A GLY* 4.5 0.2 - - - -
124B GLY* 1.3 73.0 - - - -
126B MET* 1.3 71.0 + - - +
127B PHE* 4.2 5.6 - - + -
262B GLY* 3.2 46.3 + - - +
264B GLY 5.2 1.4 + - - -
275B ASP* 5.2 1.6 - - - +
301B GLN* 3.6 17.5 - - - +
302B VAL 3.3 9.4 - - - +
303B SER* 4.4 6.5 - - - -
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Residues in contact with MET 126 (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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123B GLN 4.8 0.2 - - - +
124B GLY* 3.6 22.9 - - - +
125B LEU* 1.3 82.7 - - - +
127B PHE* 1.3 61.9 + - - +
262B GLY* 4.6 3.8 - - - +
274B VAL* 3.6 31.0 - - + +
275B ASP* 3.5 33.9 - - - +
278B ALA* 3.6 29.2 - - + +
279B ALA* 3.9 22.0 - - + +
300B ILE 3.8 0.5 - - - +
301B GLN* 3.4 3.5 - - - +
302B VAL* 2.8 43.7 + - + +
304B TYR* 3.8 14.1 - - + -
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Residues in contact with PHE 127 (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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7A PHE* 3.9 9.4 - + - -
257A GLY* 3.6 30.7 - - - -
125B LEU* 4.2 4.7 - - + -
126B MET* 1.3 76.9 - - - +
128B GLY* 1.3 58.9 + - - +
254B THR* 6.1 0.2 - - - +
255B TYR* 4.2 12.2 + - + -
259B ALA* 5.6 0.4 - - + -
260B PRO* 3.4 39.5 - - + +
261B HIS* 3.6 24.0 - - - -
262B GLY* 3.7 3.6 - - - +
279B ALA* 4.3 17.1 - - - +
282B GLY* 5.0 2.7 - - - -
299B LEU* 3.9 26.7 - - + -
300B ILE 3.2 13.2 - - - -
301B GLN* 3.2 45.1 - - + -
315B MET* 5.9 1.1 - - - -
364B PHE* 5.4 0.9 - - - -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 1.3 73.4 - - - +
129B TYR* 1.3 62.7 + - - +
255B TYR* 3.7 6.1 - - - -
282B GLY* 3.5 27.0 - - - -
283B ARG 3.8 0.7 - - - -
286B ALA* 3.9 1.8 - - - -
299B LEU* 3.4 6.3 - - - +
300B ILE* 2.8 39.9 + - - +
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Residues in contact with TYR 129 (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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128B GLY* 1.3 74.4 - - - +
130B ALA* 1.3 79.6 + - - +
131B CYS* 3.9 14.3 - - + +
133B GLU* 5.5 1.6 + - - -
139B PRO* 4.0 25.7 - - + +
255B TYR* 3.0 46.0 + + + -
258B ALA* 4.2 20.2 + - + +
259B ALA* 3.9 16.6 - - + -
282B GLY 4.4 0.2 + - - -
283B ARG* 2.9 21.3 + - - -
286B ALA* 3.5 6.1 - - - +
297B ARG* 3.3 31.6 + - + -
298B ALA 3.3 17.3 - - - -
299B LEU* 3.9 14.8 - - + -
319B PHE* 4.1 21.5 - + - -
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Residues in contact with ALA 130 (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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129B TYR* 1.3 85.8 - - - +
131B CYS* 1.3 65.4 + - - +
137B LEU* 3.5 9.4 - - + +
138B MET* 5.5 0.2 - - - +
283B ARG* 3.5 10.5 - - - +
286B ALA* 3.4 31.4 - - + +
287B LYS* 3.5 9.2 - - - +
290B VAL* 4.0 7.2 - - + -
297B ARG* 3.3 1.7 - - - +
298B ALA 3.0 30.2 + - - +
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Residues in contact with CYS 131 (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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129B TYR* 3.9 11.7 - - - +
130B ALA* 1.3 78.2 - - - +
132B ASP* 1.3 59.5 + - - +
133B GLU* 3.2 26.4 + - + +
137B LEU* 2.9 30.0 + - - +
138B MET 3.6 1.6 - - - -
139B PRO* 3.5 40.6 - - - -
290B VAL* 4.3 6.1 - - - -
296B SER 3.2 8.7 - - - +
297B ARG* 3.7 18.4 - - + -
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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