Contacts of the helix formed by residues 304 - 312 (chain C) in PDB entry 1M8V
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 ARG 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C GLU* 1.3 78.4 - - - +
305C PRO* 1.3 66.4 - - + +
306C LEU* 3.2 2.2 - - + +
307C ASP* 2.6 55.4 + - - +
308C VAL* 3.0 9.7 + - - +
434D TYR 3.8 3.6 - - - +
435D ASP* 5.9 1.3 - - + -
441D VAL* 3.9 2.2 - - - -
2P U 2.7 28.9 + - - +
3P U 3.0 34.6 + - - -
4S U 3.6 46.6 + - + +
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Residues in contact with PRO 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ARG* 1.3 86.3 - - + +
306C LEU* 1.3 63.0 + - + +
308C VAL* 3.6 2.4 + - - +
309C ILE* 3.1 34.1 + - + +
338C LEU* 5.7 2.5 - - + -
434D TYR* 3.6 21.8 - - - +
435D ASP* 3.7 16.6 - - + +
439D ASN* 3.6 37.0 - - + +
441D VAL* 3.4 21.0 - - + -
461D VAL* 3.7 17.7 - - + +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ARG* 3.2 2.0 - - + +
305C PRO* 1.3 81.8 - - + +
307C ASP* 1.3 61.2 + - - +
309C ILE* 4.4 5.8 - - + +
310C HIS* 2.9 31.6 + - - +
334C TYR* 4.4 24.6 + - + -
335C ASP 4.9 4.5 - - - +
336C ILE* 4.7 23.1 - - + +
338C LEU* 4.2 24.9 - - + -
435D ASP* 5.5 3.6 - - - +
1P U 5.3 2.0 - - - +
2P U 3.3 47.4 - - - +
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Residues in contact with ASP 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU* 3.6 12.3 + - - +
304C ARG* 2.6 62.7 + - - +
306C LEU* 1.3 71.4 - - - +
308C VAL* 1.3 53.9 + - - +
310C HIS* 3.6 1.0 - - - +
311C ARG* 2.5 51.3 + - - +
2P U 2.7 43.3 + - - +
3P U 5.4 0.5 - - - +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU* 3.5 26.2 - - - +
304C ARG 3.0 9.4 + - - +
305C PRO 3.9 1.6 - - - +
307C ASP* 1.3 78.0 - - - +
309C ILE* 1.3 64.2 + - + +
311C ARG* 3.3 16.4 + - - +
312C SER* 3.0 24.8 + - - -
372C PRO* 3.7 28.9 - - + -
441D VAL* 3.8 23.8 - - + -
459D LYS* 4.0 15.0 - - + -
461D VAL* 3.8 20.6 - - + -
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO 3.1 18.4 + - - +
306C LEU* 4.3 5.2 - - + +
308C VAL* 1.3 80.0 - - + +
310C HIS* 1.3 59.8 + - - +
312C SER* 2.9 26.7 + - - -
331C LEU* 3.5 17.7 - - + +
334C TYR* 3.9 37.3 - - + -
338C LEU* 4.0 25.1 - - + -
340C VAL* 5.6 2.9 - - + -
370C ILE* 4.0 35.0 - - + -
372C PRO* 6.1 0.2 - - - -
461D VAL* 4.3 22.2 - - + -
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Residues in contact with HIS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C LEU 2.9 22.6 + - - +
307C ASP 3.6 2.7 - - - +
309C ILE* 1.3 73.2 - - - +
311C ARG* 1.3 73.8 + - + +
312C SER 2.9 3.1 + - - -
313C LEU* 3.0 39.3 + - + +
334C TYR* 2.7 35.6 + - - +
1P U 4.2 17.9 + + - -
2P U 3.2 46.2 + + + -
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU* 3.0 33.7 + - - +
307C ASP* 2.5 51.5 + - - +
308C VAL* 3.5 22.3 + - - +
310C HIS* 1.3 79.2 - - + +
312C SER* 1.4 58.5 + - - +
313C LEU* 3.2 3.8 + - - +
315C LYS* 3.4 25.4 + - - +
372C PRO* 6.1 0.4 - - - +
459D LYS* 3.3 20.6 - - - +
2P U 5.9 0.4 - - - -
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL* 3.0 12.6 + - - +
309C ILE* 2.9 15.7 + - - -
310C HIS 2.9 0.6 + - - -
311C ARG* 1.4 74.5 + - - +
313C LEU* 1.3 67.7 + - - +
314C ASP 3.2 0.5 + - - -
315C LYS* 2.9 33.5 + - - +
317C VAL* 3.9 20.9 - - - -
331C LEU* 3.9 7.4 - - - +
372C PRO* 3.4 28.6 - - - +
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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
------------------------------------------------------------
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