Contacts of the helix formed by residues 320 - 325 (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 ILE 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C LYS* 3.5 1.8 - - - +
276C GLU* 4.1 27.4 - - + +
279C GLN* 2.9 47.2 + - + +
280C ARG* 3.6 28.5 - - + +
283C LEU* 3.3 34.8 - - + -
319C LEU* 1.3 71.2 - - - +
321C PRO* 1.3 74.8 - - + +
322C GLU* 4.3 7.2 - - + +
323C LEU* 2.8 25.8 + - + +
324C GLN 2.8 9.7 + - - -
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Residues in contact with PRO 321 (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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59B THR* 4.9 11.0 - - + +
389B GLU* 3.4 35.2 - - + +
390B ASN 5.2 1.3 - - - +
391B ILE* 3.7 27.8 - - + +
394B ARG* 5.7 0.9 - - - +
319C LEU 3.3 4.7 - - - +
320C ILE* 1.3 84.3 - - + +
322C GLU* 1.3 75.0 + - - +
323C LEU 3.0 1.0 + - - -
324C GLN* 3.1 18.6 + - + +
325C GLY* 3.1 11.6 + - - -
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 4.1 17.7 + - + +
82B GLU* 5.7 1.3 - - - +
257B ASP* 5.7 0.7 - - - +
258B GLU* 2.5 32.6 - - - +
394B ARG* 5.2 5.0 - - - +
451B ATP 3.8 27.8 + - - +
280C ARG* 5.6 2.6 + - - -
283C LEU* 3.5 32.3 - - + +
287C GLU* 4.3 9.5 - - - +
320C ILE* 3.0 7.0 + - + +
321C PRO* 1.3 86.5 - - - +
323C LEU* 1.3 58.5 + - - +
325C GLY* 3.8 1.4 + - - -
326C ARG* 3.3 24.9 + - - +
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Residues in contact with LEU 323 (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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259C ILE* 4.4 22.7 - - + -
279C GLN* 3.9 34.5 - - + +
282C LEU* 5.3 8.3 - - + -
283C LEU* 4.1 18.8 - - + -
286C VAL* 4.1 28.3 - - + -
319C LEU* 4.5 9.9 - - + -
320C ILE* 2.8 22.4 + - + +
322C GLU* 1.3 72.3 - - - +
324C GLN* 1.3 53.1 + - - +
325C GLY 2.6 17.0 + - - -
326C ARG* 2.7 14.4 + - - +
327C LEU* 3.1 27.8 + - + +
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Residues in contact with GLN 324 (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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389B GLU* 3.7 34.2 - - - +
391B ILE* 4.7 12.6 - - + +
395B ARG* 4.9 6.9 + - - +
398B THR* 5.0 2.6 + - - -
316C PRO 4.6 3.1 - - - +
317C SER* 3.6 34.3 - - - +
319C LEU* 3.1 35.5 + - + +
320C ILE 2.8 13.0 + - - +
321C PRO* 3.5 10.9 - - + +
323C LEU* 1.3 72.2 - - - +
325C GLY* 1.3 56.4 + - - +
327C LEU* 3.7 11.4 - - - +
330C ARG* 3.4 30.3 + - - +
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Residues in contact with GLY 325 (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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391B ILE* 4.1 18.4 - - - -
394B ARG* 3.7 27.9 + - - +
397B HIS* 5.1 3.3 - - - +
398B THR* 4.6 8.6 + - - -
321C PRO 3.1 11.0 + - - -
322C GLU 3.8 1.8 + - - -
323C LEU 2.6 5.7 + - - -
324C GLN* 1.3 76.2 - - - +
326C ARG* 1.3 58.9 + - - +
327C LEU 3.1 6.7 + - - -
328C PRO* 4.4 8.7 - - - +
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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