Contacts of the helix formed by residues 311 - 320 (chain C) in PDB entry 2X1L
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 ASP 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B ASP* 5.4 8.0 - - - +
18C PRO 4.4 5.8 - - - +
308C ASN* 3.6 32.1 - - + +
309C VAL 3.4 0.8 - - - -
310C VAL* 1.3 78.4 - - - +
312C PRO* 1.3 71.9 - - - +
313C VAL* 3.5 17.8 + - - +
314C ASN* 3.2 25.1 + - + +
315C LEU* 3.1 24.1 + - - +
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Residues in contact with PRO 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 3.6 16.8 - - + +
19C HIS 3.7 17.3 - - - +
20C ILE* 4.0 5.8 - - + +
23C ALA* 3.7 23.3 - - + -
81C LEU* 3.8 26.2 - - + -
85C LEU* 4.9 3.1 - - + -
310C VAL 3.2 11.0 - - - +
311C ASP* 1.3 87.4 - - - +
313C VAL* 1.3 65.3 + - + +
315C LEU* 3.4 13.2 + - + +
316C VAL* 3.1 31.1 + - - +
324C VAL* 5.5 1.7 - - + +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.8 25.6 - - + -
84C LYS* 3.7 31.6 - - + +
311C ASP* 3.2 15.9 - - - +
312C PRO* 1.3 78.7 - - + +
314C ASN* 1.3 56.9 + - - +
316C VAL* 3.4 0.7 + - - -
317C ASP* 3.1 36.2 + - - +
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Residues in contact with ASN 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ILE* 2.9 31.4 + - - +
308C ASN* 2.8 33.3 + - + +
311C ASP* 3.2 24.6 + - + +
313C VAL* 1.3 81.5 - - - +
315C LEU* 1.3 53.6 + - - +
317C ASP* 3.4 8.4 + - - +
318C THR* 2.6 45.7 + - - -
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Residues in contact with LEU 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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20C ILE* 3.7 30.3 - - + -
306C ILE* 4.5 8.5 - - + -
308C ASN 4.7 1.8 - - - +
309C VAL* 3.4 36.3 - - + +
311C ASP 3.1 17.4 + - - +
312C PRO* 3.8 7.9 - - + +
313C VAL 3.4 0.2 - - - -
314C ASN* 1.3 76.4 - - - +
316C VAL* 1.3 58.2 + - - +
318C THR* 4.4 0.9 - - - -
319C PHE* 2.8 56.5 + - + -
324C VAL* 3.4 20.0 - - + +
340C TYR* 4.5 6.3 - - + +
345C ILE* 4.0 15.9 - - + -
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Residues in contact with VAL 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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84C LYS* 3.8 26.2 - - + +
85C LEU* 3.9 25.4 - - + -
312C PRO 3.1 21.5 + - - +
313C VAL* 3.7 4.3 - - - +
315C LEU* 1.3 76.8 - - - +
317C ASP* 1.3 58.5 + - - +
320C GLY* 2.8 30.4 + - - -
321C LEU* 3.8 35.7 - - + +
324C VAL* 4.0 18.2 - - + -
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Residues in contact with ASP 317 (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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84C LYS* 2.8 26.6 + - - -
313C VAL* 3.1 33.2 + - - +
314C ASN* 3.7 9.8 - - - +
316C VAL* 1.3 75.8 - - - +
318C THR* 1.3 62.1 + - - +
320C GLY 4.8 0.5 + - - -
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Residues in contact with THR 318 (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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306C ILE* 3.8 33.8 + - + +
314C ASN* 2.6 37.5 + - - -
315C LEU* 3.8 3.6 - - - -
317C ASP* 1.3 81.0 - - - +
319C PHE* 1.3 72.5 + - + +
512C TYR* 3.9 26.3 - - + +
513C GLN 5.9 1.0 - - - -
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Residues in contact with PHE 319 (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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306C ILE* 4.0 22.2 - - + -
315C LEU* 2.8 52.0 + - + +
318C THR* 1.3 83.6 - - + +
320C GLY* 1.3 59.7 + - - +
323C GLN* 3.2 31.0 + - + +
324C VAL* 4.2 11.0 - - + -
342C GLU* 4.5 5.6 - - + -
345C ILE* 3.8 34.8 - - + -
346C ILE* 3.7 25.6 - - + -
349C VAL* 4.9 8.8 - - + +
512C TYR* 3.6 34.8 - + + -
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Residues in contact with GLY 320 (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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316C VAL* 2.8 18.1 + - - -
317C ASP 4.6 0.8 + - - -
318C THR 3.6 0.8 - - - -
319C PHE* 1.3 79.7 - - - +
321C LEU* 1.3 64.5 + - - -
323C GLN* 3.4 11.7 + - - -
324C VAL* 3.2 23.6 + - - +
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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
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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