Contacts of the strand formed by residues 124 - 131 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP 4.2 0.2 + - - -
123A GLN* 1.3 79.0 - - - +
125A LEU* 1.3 61.4 + - - -
126A MET* 3.8 13.7 - - - +
274A VAL* 5.5 0.4 - - - -
275A ASP* 4.8 5.8 - - - -
303A SER* 3.5 4.0 - - - -
304A TYR* 3.1 31.4 + - - +
8B THR* 5.7 0.2 - - - -
10B GLU* 3.8 14.1 - - - -
171B GLN* 3.8 7.9 + - - +
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Residues in contact with LEU 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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124A GLY* 1.3 73.1 - - - -
126A MET* 1.3 69.6 + - - +
127A PHE* 3.4 36.1 - - + -
262A GLY* 3.2 32.6 + - - +
264A GLY 5.5 0.9 + - - -
275A ASP* 5.3 1.6 - - - +
301A GLN* 4.8 7.4 - - + -
302A VAL 3.4 22.0 - - - +
303A SER* 3.9 17.5 - - - -
313A SER* 5.1 2.5 - - - +
7B PHE* 4.0 13.9 - - + -
8B THR* 3.3 36.1 - - + +
9B SER* 5.9 1.1 - - - -
10B GLU* 4.9 1.8 + - - +
256B GLY 4.6 1.3 - - - +
257B GLY* 4.5 7.4 - - - -
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY* 3.8 16.4 - - - +
125A LEU* 1.3 83.2 - - - +
127A PHE* 1.3 64.1 + - - +
262A GLY* 4.9 1.1 - - - +
274A VAL* 3.8 26.9 - - - +
275A ASP* 4.2 17.3 - - - +
278A ALA* 3.4 8.1 - - + +
279A ALA* 4.0 22.2 - - + +
300A ILE 3.9 0.5 - - - +
301A GLN* 3.5 3.1 - - - +
302A VAL* 2.8 76.6 + - + +
304A TYR* 3.2 28.0 - - + -
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Residues in contact with PHE 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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125A LEU* 3.4 33.4 - - + -
126A MET* 1.3 76.4 - - - +
128A GLY* 1.3 59.3 + - - +
255A TYR* 4.1 11.9 - - + -
259A ALA* 5.3 1.6 - - + -
260A PRO* 3.2 50.9 - - + +
261A HIS* 4.1 8.1 - - - -
262A GLY* 3.7 11.7 - - - +
279A ALA* 4.4 14.8 - - - +
282A GLY* 5.1 2.9 - - - -
299A LEU* 3.8 28.9 - - + -
300A ILE 3.4 1.6 - - - -
301A GLN* 3.5 26.7 - - + -
364A PHE* 5.4 1.0 - - - -
7B PHE* 4.0 11.4 - + - -
257B GLY* 3.6 17.9 - - - -
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 1.3 74.8 - - - +
129A TYR* 1.3 61.2 + - - -
255A TYR* 3.7 5.6 - - - -
282A GLY* 3.6 27.0 - - - -
283A ARG 3.8 0.2 - - - -
286A ALA* 3.8 7.0 - - - -
298A ALA 3.9 0.2 - - - +
299A LEU* 3.3 8.5 - - - +
300A ILE* 2.8 36.7 + - - +
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Residues in contact with TYR 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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128A GLY* 1.3 75.2 - - - +
130A ALA* 1.3 76.4 + - - +
131A CYS* 3.9 22.6 - - + +
139A PRO* 4.3 7.4 - - + -
255A TYR* 3.0 47.0 + + + -
258A ALA* 4.3 26.2 + - + +
259A ALA* 3.9 17.7 - - + -
283A ARG* 3.1 20.8 + - - +
286A ALA* 3.6 5.5 - - - +
297A ARG* 3.1 34.9 + - + -
298A ALA 3.2 24.9 - - - -
299A LEU* 4.0 12.3 - - + -
319A PHE* 4.2 17.5 - + - -
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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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129A TYR* 1.3 85.4 - - - +
131A CYS* 1.3 62.8 + - - +
137A LEU* 3.4 9.0 - - + +
138A MET* 5.4 0.4 - - - +
139A PRO* 5.7 0.2 - - - -
283A ARG* 3.6 12.8 - - - +
286A ALA* 3.3 31.4 - - + +
287A LYS* 3.6 6.7 - - - -
290A VAL* 3.6 8.7 - - + +
297A ARG* 3.4 2.6 - - - +
298A ALA 3.1 29.1 + - - +
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Residues in contact with CYS 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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129A TYR* 3.9 13.0 - - - +
130A ALA* 1.3 76.3 - - - +
132A ASP* 1.3 59.3 - - - +
133A GLU* 3.3 22.0 + - + +
137A LEU* 2.9 31.8 + - - -
138A MET* 3.6 2.0 - - - +
139A PRO* 3.4 43.5 - - - -
290A VAL* 4.3 5.8 - - - -
296A SER 3.4 7.4 - - - +
297A ARG* 3.6 19.3 - - + -
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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