Contacts of the helix formed by residues 313 - 320 (chain A) in PDB entry 1U5U
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 SER 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A PRO 4.2 0.6 + - - -
312A LEU* 1.3 77.2 - - - +
314A PRO* 1.3 76.4 - - - +
315A ASP* 2.4 26.2 + - - -
316A VAL* 2.9 27.3 + - - -
317A LEU* 3.0 11.4 + - - +
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Residues in contact with PRO 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU 3.2 6.0 - - - +
313A SER* 1.3 87.8 - - - +
315A ASP* 1.3 60.0 + - + +
317A LEU* 3.6 7.1 + - + +
318A GLU* 3.1 27.8 + - - +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A SER* 2.4 31.7 + - - -
314A PRO* 1.3 77.5 - - + +
316A VAL* 1.3 71.9 + - - +
318A GLU* 3.7 6.2 - - - +
319A LYS* 3.2 31.3 + - + +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.4 30.5 - - - +
127A ASP* 3.7 7.4 - - - +
312A LEU* 3.9 17.3 - - + -
313A SER* 2.9 26.9 + - - +
315A ASP* 1.3 83.6 - - - +
317A LEU* 1.3 63.5 + - - +
319A LYS* 3.4 20.8 - - - +
320A THR* 2.7 26.5 + - - -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.9 20.8 + - - -
70A GLY 4.2 6.1 - - - +
71A THR* 3.5 37.5 - - - +
72A GLY* 3.8 5.4 - - - +
100A ARG* 6.4 0.4 - - + -
101A LEU 3.9 20.0 - - - +
102A ARG* 3.9 25.1 - - + +
312A LEU* 3.8 29.7 - - + +
313A SER 3.0 14.7 + - - +
314A PRO* 4.0 8.3 - - + +
316A VAL* 1.3 75.7 - - - +
318A GLU* 1.3 60.7 + - - +
320A THR* 3.2 13.7 + - - +
322A PHE* 5.7 1.1 - - + -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE 4.8 0.5 - - - +
63A ARG* 2.9 62.4 + - - +
64A ARG* 2.9 42.6 + - - +
68A THR 5.0 0.2 - - - +
102A ARG* 4.6 1.8 + - - +
314A PRO 3.1 16.7 + - - +
315A ASP* 3.7 9.2 - - - +
316A VAL 3.2 0.2 - - - -
317A LEU* 1.3 81.0 - - - +
319A LYS* 1.3 56.4 + - + +
360A ARG* 3.0 16.2 + - - +
367A LEU* 3.8 22.7 - - + +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.2 42.9 + - + +
128A SER* 4.8 2.1 + - - -
315A ASP* 3.2 17.3 + - + +
316A VAL* 3.4 29.2 - - - +
318A GLU* 1.3 77.4 - - + +
320A THR* 1.3 65.2 + - - +
321A ALA* 3.5 5.9 + - - +
360A ARG* 4.2 8.5 + - - +
364A ILE* 4.1 33.8 - - + +
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.7 26.7 + - - -
100A ARG* 2.8 26.6 + - + -
122A LYS* 4.2 8.1 - - - -
126A SER 4.0 10.3 - - - +
127A ASP* 3.2 15.5 - - - +
312A LEU* 4.4 0.5 - - - +
316A VAL 2.7 21.6 + - - -
317A LEU* 3.2 16.5 + - + -
319A LYS* 1.3 77.9 - - - +
321A ALA* 1.3 61.7 + - - +
322A PHE* 3.7 31.4 + - + -
360A ARG* 3.3 5.7 + - - -
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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