Contacts of the strand formed by residues 97 - 102 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.2 43.5 + - + +
27A THR* 5.0 0.8 - - - +
50G LYS* 4.7 10.2 - - - -
90G LEU* 4.0 5.4 - - - -
95G VAL 3.7 10.1 - - - +
96G ALA* 1.3 80.3 - - - +
98G ILE* 1.3 68.3 - - - +
162G ASP* 3.4 27.5 + - + +
163G LYS* 4.1 8.5 - - - +
232G ILE* 3.1 4.8 - - - -
233G THR* 2.9 48.0 + - - +
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.6 9.7 - - - +
35A HIS* 2.9 20.8 + - - -
88G LEU* 4.4 4.0 - - + +
90G LEU* 4.0 13.7 - - + +
97G GLN* 1.3 70.7 - - - +
99G SER* 1.3 59.8 + - - +
100G ASP 4.2 5.6 - - - +
101G TYR* 3.8 29.2 - - + -
161G THR 3.6 14.1 - - - +
162G ASP* 3.0 13.7 + - - +
163G LYS 3.4 3.1 - - - +
164G LYS* 3.1 49.6 - - - +
165G VAL* 3.5 14.1 - - + +
230G THR* 4.3 14.4 - - + -
231G VAL 3.7 3.8 - - - -
232G ILE* 4.6 4.9 - - + +
245G ILE* 6.3 1.1 - - + -
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Residues in contact with SER 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.3 9.9 + - - -
26A VAL* 3.8 13.0 - - - +
35A HIS* 3.7 12.8 - - - -
37A LYS* 2.8 50.4 + - - +
59A GLY* 5.3 1.4 + - - -
97G GLN 3.3 0.6 + - - -
98G ILE* 1.3 75.2 - - - +
100G ASP* 1.3 59.2 + - - +
101G TYR* 5.1 0.2 - - - -
231G VAL* 2.8 19.0 + - - +
233G THR* 3.3 31.3 - - - +
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Residues in contact with ASP 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 3.9 8.7 + - - +
58A LYS* 2.7 34.8 + - - +
59A GLY 5.6 1.6 + - - -
4F ASP 3.5 3.8 - - - +
5F ILE* 3.5 15.1 - - + +
6F ASN* 4.0 2.6 - - - +
98G ILE* 3.9 0.7 - - - +
99G SER* 1.3 76.8 - - - +
101G TYR* 1.3 96.8 + - - +
104G ARG* 3.0 25.3 + - - -
230G THR* 3.7 3.3 - - - +
231G VAL* 2.8 45.7 + - + +
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Residues in contact with TYR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 2.7 40.1 + + - -
59A GLY* 3.1 10.9 - - - -
60A THR* 2.6 38.0 - - + +
225A SER* 4.2 3.4 - - - -
5F ILE* 4.5 3.6 - - - +
98G ILE* 3.8 15.5 - - + -
100G ASP* 1.3 97.5 + - - +
102G TYR* 1.3 63.7 + - - +
103G PRO 4.4 0.7 - - - -
104G ARG* 3.0 35.5 + - - +
157G LEU* 3.6 21.5 - - + -
160G PRO* 3.4 12.7 - - + +
165G VAL* 4.0 13.2 - - + -
167G TRP* 3.8 17.5 - - + -
229G ALA 3.1 13.9 - - - +
230G THR* 4.7 1.6 - - - -
231G VAL 4.9 0.2 - - - +
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Residues in contact with TYR 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ALA 3.6 23.8 - - - +
4F ASP* 3.4 41.0 + - + -
5F ILE* 4.2 14.6 - - + -
101G TYR* 1.3 74.6 - - - +
103G PRO* 1.3 87.2 - - + +
104G ARG* 3.6 25.1 - - + -
167G TRP* 3.7 3.3 - - - -
227G ASP 4.4 0.3 - - - +
228G PHE* 3.5 1.7 - - - -
229G ALA* 2.8 40.4 + - + +
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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