Contacts of the strand formed by residues 129 - 137 (chain B) in PDB entry 4IYM
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 ILE 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A VAL* 5.1 2.0 - - + -
124B GLY* 3.0 19.3 + - - -
125B ALA* 3.0 16.7 + - + -
126B GLY* 3.1 27.3 + - - +
127B PRO* 3.6 23.1 - - + +
128B GLY* 1.3 77.0 - - - +
130B ASP* 1.3 68.6 - - - +
131B MSE 5.2 1.1 - - + -
477B THR* 3.5 31.9 - - + -
478B SER 3.3 6.7 - - - +
479B ARG* 3.7 38.1 - - + +
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Residues in contact with ASP 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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121B PHE* 4.0 22.6 - - + -
122B THR 3.5 7.6 - - - +
123B GLU* 3.3 17.6 - - - +
124B GLY* 3.0 22.0 + - - -
128B GLY 5.0 3.9 - - - +
129B ILE* 1.3 77.7 + - - +
131B MSE 1.3 60.2 + - - +
132B TYR* 4.4 6.7 - - + -
476B ILE 3.8 0.5 - - - +
477B THR* 3.5 2.4 - - - -
478B SER* 2.9 41.8 + - - +
134C ILE* 5.7 0.9 - - - +
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Residues in contact with MSE 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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441A VAL 4.2 4.7 - - - +
442A PRO* 4.1 6.3 - - + -
443A LEU* 3.4 53.8 - - + +
446A HIS* 3.6 31.3 - - + +
121B PHE* 3.7 0.3 - - - -
122B THR* 2.8 37.7 + - - +
125B ALA* 3.9 16.8 - - + +
129B ILE* 5.2 1.1 - - + -
130B ASP* 1.3 74.5 - - - +
132B TYR* 1.3 64.1 + - - +
475B THR* 4.1 11.9 - - + -
476B ILE 3.3 9.6 - - - +
477B THR* 3.4 29.4 - - + +
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Residues in contact with TYR 132 (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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425A ALA* 5.7 0.9 - - - +
435A VAL* 5.5 1.7 - - - +
446A HIS* 4.6 2.5 - - - -
120B GLU 3.2 13.0 - - - +
121B PHE* 3.5 31.0 - + + -
130B ASP* 4.4 3.4 - - + -
131B MSE 1.3 86.1 - - - +
133B SER* 1.3 63.2 + - - +
134B ILE* 4.6 0.2 - - + -
475B THR* 3.4 4.4 - - - -
476B ILE* 2.7 89.5 + - + +
478B SER* 4.2 18.3 + - - -
121C PHE* 3.4 38.8 - + + -
132C TYR* 6.6 0.2 - + - -
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Residues in contact with SER 133 (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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446A HIS* 4.7 5.6 + - - -
119B SER* 2.5 26.4 + - - -
120B GLU* 3.0 34.0 + - - +
132B TYR* 1.3 77.2 - - - +
134B ILE* 1.3 63.0 + - - +
135B ARG* 5.7 0.4 - - - +
473B THR* 3.8 19.7 - - - +
474B LYS 2.9 12.8 - - - -
475B THR* 3.8 9.2 - - - +
121C PHE* 3.9 9.9 - - - +
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Residues in contact with ILE 134 (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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425A ALA 5.2 1.6 - - - +
426A SER* 5.4 1.6 - - - -
119B SER* 3.4 4.5 - - - +
132B TYR* 4.6 1.1 - - + -
133B SER* 1.3 79.8 - - - +
135B ARG* 1.3 69.0 + - - +
136B GLN* 3.6 13.4 + - + +
472B ARG 3.5 2.4 - - - +
473B THR* 3.6 1.7 - - - -
474B LYS* 2.7 47.0 + - + +
476B ILE* 3.6 31.4 - - + -
121C PHE* 3.7 25.6 - - + -
123C GLU* 3.6 49.4 - - + +
130C ASP* 5.9 0.7 - - - +
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Residues in contact with ARG 135 (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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116B LEU 2.9 26.1 + - - -
117B GLN* 3.1 35.4 + - + +
118B LYS 3.1 26.3 + - - -
119B SER* 4.1 10.8 - - - +
133B SER* 5.7 0.4 - - - +
134B ILE* 1.3 79.5 - - - +
136B GLN* 1.3 61.7 + - - +
464B THR* 4.6 3.6 + - - -
467B ILE* 3.5 25.6 - - - +
468B LYS* 3.7 41.3 - - - +
471B THR* 3.9 17.9 + - - +
472B ARG 3.5 4.0 - - - -
473B THR* 4.5 15.9 - - + +
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Residues in contact with GLN 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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426A SER* 2.9 23.7 + - - +
428A ILE 4.5 0.2 - - - +
451A TRP* 3.2 22.7 - - + -
117B GLN* 4.7 0.2 - - - -
134B ILE* 3.9 14.6 - - + +
135B ARG* 1.3 77.7 - - - +
137B PRO* 1.3 75.1 - - + +
471B THR* 3.2 8.3 - - - -
472B ARG* 2.8 34.7 + - - +
474B LYS* 2.8 31.0 + - + +
123C GLU* 3.1 33.0 + - - +
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Residues in contact with PRO 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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52B GLN* 3.7 11.4 - - - +
56B ALA* 3.8 19.3 - - + -
117B GLN* 5.0 2.0 - - - +
135B ARG 4.9 0.2 - - - +
136B GLN* 1.3 94.2 - - + +
138B VAL* 1.3 60.2 + - - +
139B GLY 3.5 1.1 + - - +
164B CYS 3.5 22.4 - - - +
165B GLY* 3.6 20.0 - - - +
166B ASN* 3.2 16.2 - - - +
470B TRP 4.1 4.0 - - - +
472B ARG* 3.2 19.5 + - - -
123C GLU* 6.1 0.2 - - - +
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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