Contacts of the strand formed by residues 3 - 8 (chain C) in PDB entry 4IGM
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 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LYS* 1.3 79.7 - - + +
4C ASP* 1.3 68.1 + - - +
5C ILE* 4.7 2.0 - - + +
68C VAL* 5.0 0.2 - - - -
69C THR* 5.4 0.2 - - - -
70C VAL* 3.2 36.1 - - + +
72C ALA* 5.4 1.3 - - + +
287C ILE* 5.2 1.6 - - - +
288C LEU* 3.4 22.4 - - - +
320C LYS 2.8 20.9 + - - +
321C ALA* 3.6 22.4 - - + +
324C ALA* 3.7 21.1 - - + -
325C LEU* 3.5 41.7 - - + -
328C LEU* 5.2 9.6 - - + -
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Residues in contact with ASP 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LYS 4.1 0.2 + - - -
3C ILE* 1.3 73.9 - - - +
5C ILE* 1.3 55.7 + - - +
6C HIS 3.1 13.5 + - - +
7C SER* 4.1 4.5 + - - -
68C VAL* 4.2 16.1 - - + +
70C VAL 2.7 13.9 + - - +
71C GLN* 3.4 10.0 + - + +
72C ALA 2.8 31.7 + - - +
288C LEU* 3.8 7.0 - - + -
289C GLY* 3.0 7.8 - - - -
290C THR* 2.7 55.0 + - - +
292C TYR* 4.1 8.3 - - - +
301C PRO* 5.8 1.5 - - + +
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Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.0 3.6 - - + +
4C ASP* 1.3 70.7 + - - +
6C HIS* 1.3 59.2 + - + +
7C SER 3.9 1.4 + - - -
72C ALA* 3.7 20.0 - - + +
74C SER* 5.6 0.5 + - - -
114C LEU* 4.1 11.3 - - + +
172C PHE* 4.2 21.5 - - + -
221C CYS* 4.9 2.0 - - - -
265C ASP* 4.2 22.9 - - + -
287C ILE* 3.9 17.0 - - + -
288C LEU 3.1 23.1 + - - +
324C ALA* 4.4 12.3 - - + -
327C PHE* 3.8 21.8 - - + -
328C LEU* 3.7 44.4 - - + -
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Residues in contact with HIS 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 3.1 10.1 + - - +
5C ILE* 1.3 80.7 - - + +
7C SER* 1.3 62.7 + - - +
8C HIS* 3.2 14.4 - + - -
74C SER* 5.5 0.4 - - - -
172C PHE* 3.8 17.0 - + + -
174C HIS* 2.9 15.5 + + - -
223C ALA* 4.0 4.5 - - + -
224C HIS* 3.7 22.9 - + - -
265C ASP* 3.0 21.9 + - - +
267C LEU* 4.2 5.0 - - + +
289C GLY* 3.8 16.6 - - - -
291C ASP* 2.8 35.0 + - + -
401C ZN 2.1 36.4 - - - -
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 4.1 7.9 - - - -
5C ILE 4.0 0.4 + - - -
6C HIS* 1.3 79.2 - - - +
8C HIS* 1.3 67.7 + - - +
59C ARG* 3.1 20.5 + - - -
71C GLN* 3.6 14.6 - - - +
72C ALA 3.0 18.3 + - - +
73C LEU* 4.0 0.5 - - - +
74C SER* 2.9 29.6 + - - -
292C TYR* 3.4 21.8 - - - -
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Residues in contact with HIS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C HIS* 3.1 10.9 + + - -
7C SER* 1.3 74.5 - - - +
9C ILE* 1.3 56.0 + - - +
53C CYS* 4.6 2.1 - - - +
59C ARG* 2.7 25.1 + - - -
74C SER* 3.0 16.7 + - - +
75C THR 3.0 20.6 + - - -
76C VAL* 4.1 12.8 - - + -
77C PRO* 3.9 7.6 - - + +
142C GLN* 3.1 26.2 - - - -
174C HIS* 3.4 10.3 - + - -
291C ASP* 3.2 9.9 - - - -
292C TYR 2.9 9.7 + - - +
293C PRO* 3.5 11.4 - - - +
294C PHE* 4.0 28.0 - + + -
401C ZN 2.3 34.1 - - - -
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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