Contacts of the strand formed by residues 310 - 315 (chain C) in PDB entry 5H1C
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 310 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C ARG* 2.3 36.4 + - - +
131C THR* 3.2 22.2 - - - +
132C GLY 3.4 0.6 - - - +
302C LEU* 5.9 2.5 - - + -
303C ARG 3.7 5.2 - - - +
304C LYS* 3.5 32.2 - - - +
305C GLY 3.8 0.7 - - - +
307C GLY 4.2 6.3 + - - -
308C GLU* 3.0 21.6 + - - +
309C THR* 1.3 84.7 + - - +
311C ILE* 1.3 64.3 + - - +
312C CYS 4.1 0.2 - - - -
325C ALA 3.4 0.3 - - - +
326C MET* 3.1 8.5 - - - +
327C PHE* 2.9 50.6 + - + +
329C ILE* 3.3 26.0 - - + +
401C ANP 2.3 35.7 + - - -
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Residues in contact with ILE 311 (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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301C TYR 3.3 1.7 - - - +
302C LEU* 3.2 8.3 - - - -
303C ARG* 2.8 78.4 + - + +
304C LYS 5.2 1.1 - - - +
305C GLY* 5.1 8.3 - - - +
310C ARG* 1.3 74.1 - - - +
312C CYS* 1.3 72.7 + - - +
313C GLN* 5.0 0.8 - - + +
324C GLU* 4.4 10.5 - - + +
325C ALA 3.3 6.1 - - - +
326C MET* 3.4 33.2 - - + -
327C PHE* 4.9 0.2 - - - -
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Residues in contact with CYS 312 (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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109C LEU* 3.9 17.7 - - + -
112C LEU* 3.7 27.1 - - + -
113C LEU* 5.5 1.3 - - - -
300C LEU* 3.6 35.2 - - - -
301C TYR 3.3 4.5 - - - -
302C LEU* 3.6 19.0 - - + +
310C ARG 4.1 0.8 - - - -
311C ILE* 1.3 74.2 - - - +
313C GLN* 1.3 72.4 + - - +
314C ILE* 4.9 0.9 - - - -
324C GLU* 3.0 9.7 - - - +
325C ALA 2.9 29.8 + - - +
327C PHE* 4.3 3.4 - - + -
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Residues in contact with GLN 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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300C LEU* 3.5 0.5 - - - -
301C TYR* 2.8 66.8 + - + +
303C ARG* 3.7 26.3 - - - +
311C ILE* 5.0 2.9 - - + +
312C CYS* 1.3 82.2 - - - +
314C ILE* 1.3 69.3 + - - +
315C TYR* 4.2 16.3 + - - -
322C GLU* 3.0 25.7 - - + +
323C ALA 3.3 12.6 - - - +
324C GLU* 4.3 9.8 + - + +
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Residues in contact with ILE 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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112C LEU* 3.7 30.1 - - + +
113C LEU* 4.9 3.6 - - + -
299C ARG 3.6 7.6 - - - +
300C LEU* 4.0 15.7 - - + -
312C CYS* 5.4 1.1 - - - -
313C GLN* 1.3 79.7 - - - +
315C TYR* 1.3 81.3 + - - +
317C SER* 3.3 25.6 - - - +
320C LEU* 4.2 14.1 - - + +
321C PRO 3.8 19.5 - - - +
322C GLU* 3.9 24.7 - - - +
323C ALA* 3.3 26.6 + - + +
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Residues in contact with TYR 315 (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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129B PHE* 5.5 4.7 - + + -
130B ARG* 3.0 47.8 + - - +
304B LYS* 5.0 0.2 - - - -
126C PHE* 4.1 17.0 - + - -
299C ARG* 2.9 53.3 + - + +
300C LEU 4.6 0.2 - - - -
301C TYR* 3.5 46.2 - + + -
313C GLN* 4.2 16.5 + - - -
314C ILE* 1.3 80.9 - - - +
316C ASP* 1.3 71.3 + - + +
317C SER 3.0 3.8 + - - -
322C GLU* 5.8 1.8 - - - -
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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