Contacts of the strand formed by residues 304 - 309 (chain C) in PDB entry 1G3I
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 LEU 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA* 4.6 24.7 - - + -
31C LEU* 5.3 5.2 - - + +
34C ARG* 3.5 22.8 - - - +
50C PRO* 4.3 10.3 - - + -
51C LYS 4.7 2.5 - - - +
52C ASN* 4.0 19.1 - - - +
53C ILE* 4.6 4.7 - - + -
70C LEU* 4.3 12.1 - - + -
252C GLY 2.8 12.8 + - - +
253C ILE* 3.4 29.0 - - + +
254C VAL 3.0 24.4 + - - -
303C ILE* 1.3 72.3 - - - +
305C PHE* 1.3 72.7 + - - +
306C ILE* 4.2 11.9 - - + -
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Residues in contact with PHE 305 (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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52C ASN* 2.4 43.9 + - + +
53C ILE 3.1 21.5 + - - -
100C ILE* 4.6 5.6 - - + -
254C VAL* 3.5 33.9 - - + -
256C ILE* 4.2 14.6 - - + -
282C LEU* 6.1 0.2 - - + -
285C LEU* 3.8 48.9 - - + -
286C VAL* 3.8 27.6 - - + -
300C THR 4.3 2.5 - - - -
303C ILE* 3.3 39.0 - - + -
304C LEU* 1.3 71.1 - - - +
306C ILE* 1.3 66.9 + - - +
307C ALA* 4.1 1.3 - - + -
327C LEU* 5.1 4.3 - - + -
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Residues in contact with ILE 306 (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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27C VAL* 3.7 26.2 - - + -
53C ILE* 3.4 18.8 - - + +
55C MET* 3.1 37.9 - - + -
67C ALA* 4.4 9.9 - - + -
70C LEU* 4.3 4.0 - - + -
253C ILE* 3.8 24.0 - - + -
254C VAL 2.8 8.9 + - - +
255C PHE* 3.1 22.8 - - + -
256C ILE* 2.8 30.0 + - - -
304C LEU* 4.2 11.9 - - + -
305C PHE* 1.3 82.2 - - - +
307C ALA* 1.3 54.7 + - - +
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Residues in contact with ALA 307 (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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53C ILE 2.9 7.2 + - - +
54C LEU* 3.0 20.6 - - + +
55C MET* 2.8 26.7 + - - +
256C ILE* 3.4 16.2 - - + +
259C ILE* 4.0 24.7 - - + -
305C PHE* 4.1 1.5 - - + +
306C ILE* 1.3 74.6 - - - +
308C SER* 1.3 60.8 + - - +
327C LEU* 4.1 15.9 - - + +
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Residues in contact with SER 308 (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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54C LEU* 4.5 1.6 - - - -
55C MET* 3.4 8.1 - - - +
63C LYS* 3.9 15.2 - - - +
255C PHE* 3.3 29.2 - - - -
256C ILE 2.8 8.8 + - - -
257C ASP* 2.6 23.3 + - - -
258C GLU 3.4 1.8 + - - -
259C ILE* 3.0 31.9 + - - +
306C ILE 4.2 0.4 + - - -
307C ALA* 1.3 73.7 - - - +
309C GLY* 1.3 61.6 + - - +
452C ATP 3.5 8.7 + - - -
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Residues in contact with GLY 309 (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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55C MET 3.2 4.4 + - - -
56C ILE* 3.2 3.6 - - - -
57C GLY 3.0 21.6 + - - -
63C LYS* 4.3 4.4 - - - +
258C GLU* 4.4 4.3 - - - -
260C ASP* 3.3 17.5 - - - -
308C SER* 1.3 82.8 + - - +
310C ALA* 1.3 60.1 + - - -
311C PHE* 3.1 19.6 - - - -
452C ATP 5.9 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