Contacts of the strand formed by residues 97 - 102 (chain C) in PDB entry 3M4D
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 GLN 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS* 3.9 17.7 + - - -
90C LEU* 4.1 1.6 - - - -
95C VAL 3.7 9.9 + - - +
96C ALA* 1.3 80.1 - - - +
98C ILE* 1.3 69.5 + - - +
99C SER 3.4 0.2 + - - -
162C ASP* 3.1 33.1 + - + +
163C LYS* 4.1 4.5 - - - +
232C ILE* 3.2 7.4 - - - -
233C THR* 2.9 41.0 + - - +
26D VAL* 3.1 40.8 + - + +
27D THR* 4.8 1.2 - - - +
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Residues in contact with ILE 98 (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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88C LEU* 4.2 5.8 - - + +
90C LEU* 4.2 12.3 - - + -
97C GLN* 1.3 72.2 - - - +
99C SER* 1.3 60.2 + - - +
100C ASP 4.3 2.5 - - - +
101C TYR* 3.9 29.6 - - + -
161C THR 3.7 14.8 - - - +
162C ASP* 3.0 13.2 + - - +
163C LYS 3.5 5.4 - - - +
164C LYS* 3.4 43.3 - - - +
165C VAL* 3.5 17.5 - - + +
230C THR* 4.4 11.9 - - + -
231C VAL 3.6 7.4 - - - +
232C ILE* 4.5 5.6 - - + +
245C ILE* 5.9 0.9 - - + -
26D VAL* 3.6 9.2 - - - +
35D HIS* 3.0 20.4 + - - -
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Residues in contact with SER 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN 3.4 0.6 + - - -
98C ILE* 1.3 73.7 - - - +
100C ASP* 1.3 60.7 + - - +
101C TYR* 4.8 0.5 - - - -
231C VAL* 2.7 18.5 + - - +
233C THR* 3.4 30.9 - - - +
24D ASP* 3.4 9.9 + - - -
26D VAL* 3.8 13.2 - - - +
35D HIS* 3.7 12.0 - - - -
37D LYS* 2.8 44.2 + - - +
59D GLY 5.4 1.2 + - - -
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Residues in contact with ASP 100 (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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5B ILE* 3.7 15.2 - - + +
6B ASN* 3.9 2.6 - - - +
98C ILE* 3.9 0.7 - - - +
99C SER* 1.3 80.7 - - - +
101C TYR* 1.3 86.7 + - - +
104C ARG* 3.0 24.0 + - - -
230C THR* 3.7 3.5 - - - +
231C VAL* 2.8 46.5 + - + +
37D LYS* 3.9 11.5 + - - +
58D LYS* 2.7 35.7 + - - +
59D GLY 5.6 1.4 + - - -
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Residues in contact with TYR 101 (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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5B ILE* 4.6 3.5 - - - +
98C ILE* 3.9 14.1 - - + -
100C ASP* 1.3 95.6 + - - +
102C TYR* 1.3 63.1 + - - +
103C PRO 4.5 0.4 - - - -
104C ARG* 3.0 36.7 + - - +
157C LEU* 3.6 28.9 - - + -
160C PRO* 3.5 19.1 - - + -
165C VAL* 3.9 14.4 - - + -
167C TRP* 3.7 18.2 - - + -
229C ALA 3.2 13.0 - - - +
230C THR* 4.7 0.9 - - - -
35D HIS* 2.7 39.0 + + - -
59D GLY* 3.1 14.3 - - - -
60D THR* 3.1 15.4 - - - +
225D SER* 4.2 9.0 - - - -
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Residues in contact with TYR 102 (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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1B ALA 3.9 15.7 - - - +
4B ASP* 3.4 44.0 + - + -
5B ILE* 4.3 13.9 - - + -
101C TYR* 1.3 74.2 - - - +
103C PRO* 1.3 86.8 - - + +
104C ARG* 3.6 25.1 - - + -
167C TRP* 3.7 2.9 - - - -
227C ASP 4.4 0.7 - - - +
228C PHE* 3.5 1.7 - - - -
229C ALA* 2.9 39.4 + - + +
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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