Contacts of the helix formed by residues 311 - 316 (chain C) in PDB entry 3RMD
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 LYS 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C GLY* 4.7 3.8 - - - -
308C PRO* 3.1 44.2 + - + +
309C ILE 3.2 0.6 - - - -
310C SER* 1.3 77.7 - - - +
312C LEU* 1.3 58.0 + - - +
313C ARG 3.2 1.3 - - - -
314C GLU* 2.9 20.0 - - + +
315C SER* 2.5 45.5 + - - +
820C ASP* 5.4 5.8 - - - +
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C TYR* 3.7 48.7 - - + -
306C ASP 5.1 4.9 - - - +
308C PRO 3.2 10.4 + - - +
309C ILE* 2.8 24.1 + - + +
311C LYS* 1.3 71.3 - - - +
313C ARG* 1.3 69.1 + - - +
315C SER* 4.2 3.8 - - - -
316C ASN* 3.1 38.8 + - + +
319C ARG* 4.5 4.7 - - + -
320C TYR* 3.2 34.4 - - + +
323C TYR* 4.9 12.3 - - + -
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Residues in contact with ARG 313 (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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118C THR* 2.7 30.4 + - - +
134C ASP* 3.5 25.3 + - - +
150C ASP* 4.4 0.2 + - - -
151C LEU 2.7 28.3 + - - -
152C LEU 4.6 2.8 + - - -
153C ASN* 4.1 2.8 - - - +
154C SER* 2.7 38.5 + - - +
156C TYR* 4.6 4.6 + - - +
157C GLY 2.9 21.1 + - - -
159C VAL* 3.9 6.5 - - - +
309C ILE 4.1 0.4 + - - -
310C SER 4.4 1.3 - - - +
312C LEU* 1.3 83.0 - - - +
314C GLU* 1.3 70.1 + - - +
317C HIS* 3.0 56.6 + - - +
320C TYR* 3.4 27.6 - - + -
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Residues in contact with GLU 314 (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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118C THR* 4.9 1.7 - - - +
156C TYR* 2.7 30.4 - - - +
157C GLY* 5.6 3.6 - - - -
159C VAL* 4.3 15.5 - - + +
310C SER 3.2 8.3 - - - +
311C LYS* 2.9 36.5 - - + +
313C ARG* 1.3 79.9 - - - +
315C SER* 1.3 76.1 + - - +
316C ASN 3.1 1.4 + - - -
317C HIS* 3.7 5.5 + - - +
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Residues in contact with SER 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASP 5.6 5.6 - - - -
307C GLY* 6.0 1.6 - - - -
311C LYS* 2.5 35.8 + - - +
312C LEU* 4.1 4.3 - - - -
314C GLU* 1.3 83.2 - - - +
316C ASN* 1.3 64.7 + - - +
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Residues in contact with ASN 316 (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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312C LEU* 3.1 21.6 + - + +
315C SER* 1.3 83.4 - - - +
317C HIS* 1.3 60.9 + - - +
318C GLN* 3.0 11.8 + - - +
319C ARG* 3.1 33.5 + - + +
320C TYR 3.1 15.8 + - - -
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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