Contacts of the helix formed by residues 312 - 322 (chain B) in PDB entry 3LKB
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 THR 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.7 10.3 - - - -
310B ARG* 4.9 6.7 - - + -
311B ILE* 1.3 76.7 - - - +
313B ASN* 1.3 88.0 + - - +
314B GLU* 3.1 13.7 + - + +
315B THR* 3.0 46.4 + - + +
316B VAL* 3.0 25.6 + - - +
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Residues in contact with ASN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE 4.6 4.5 - - - +
77B PRO* 3.6 28.8 - - + +
97B LEU 3.1 17.4 + - - -
98B ARG* 2.9 33.9 + - - +
99B ILE* 4.3 4.7 - - + -
100B PRO* 3.6 8.4 - - + +
312B THR* 1.3 100.1 + - - +
314B GLU* 1.3 71.0 + - - +
317B TYR* 3.2 24.3 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 5.4 13.0 - - + -
312B THR* 3.1 11.3 + - + +
313B ASN* 1.3 96.9 + - - +
315B THR* 1.3 60.2 + - + +
317B TYR* 3.4 8.7 + - - +
318B GLN* 3.1 33.2 + - + +
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Residues in contact with THR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ALA* 3.6 10.9 - - - +
308B PHE* 3.7 42.1 - - + -
310B ARG* 2.8 34.6 + - + +
312B THR* 3.0 35.9 + - + +
314B GLU* 1.3 75.1 - - + +
316B VAL* 1.3 60.7 + - - +
318B GLN* 3.3 6.8 + - + +
319B ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.0 21.1 - - + +
78B VAL* 4.4 11.4 - - + -
100B PRO* 4.1 15.5 - - + -
297B ALA* 5.3 0.7 - - - +
300B ALA* 4.0 17.4 - - + +
301B ILE* 3.9 31.0 - - + -
304B ALA* 4.3 6.5 - - + -
311B ILE* 4.4 6.7 - - + -
312B THR 3.0 21.2 + - - +
313B ASN 4.1 2.7 - - - +
315B THR* 1.3 75.9 + - - +
317B TYR* 1.3 58.4 + - - +
319B ALA* 3.2 4.9 + - - +
320B ILE* 2.9 34.5 + - + +
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ARG 5.6 0.2 - - - +
100B PRO* 3.7 13.9 - - + +
117B ASP* 3.5 26.9 + - + +
118B TYR* 3.5 33.2 - + + -
120B PHE* 4.1 13.9 - + - -
313B ASN 3.2 17.8 + - - +
314B GLU* 3.5 6.3 - - - +
316B VAL* 1.3 79.9 - - - +
318B GLN* 1.3 85.3 + - - +
320B ILE* 3.1 6.3 + - - +
321B VAL* 3.0 48.4 + - + +
347B LYS* 3.4 34.5 + - + +
350B HIS* 5.4 1.1 - - - -
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ARG* 4.9 4.8 + - - +
308B PHE* 3.9 26.9 - - + -
314B GLU* 3.1 20.2 + - + +
315B THR* 3.7 7.6 - - + +
316B VAL 3.3 0.2 - - - -
317B TYR* 1.3 97.3 - - - +
319B ALA* 1.3 61.4 + - - +
321B VAL* 3.7 13.4 + - - +
322B GLY* 3.3 20.4 + - - -
347B LYS* 5.5 7.2 - - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ALA* 3.5 26.9 - - - +
303B ARG* 3.9 16.8 - - + -
304B ALA* 3.9 11.4 - - - +
307B ARG* 4.2 13.3 + - - +
308B PHE* 5.1 0.4 - - + -
315B THR 3.0 16.6 + - - +
316B VAL 3.6 3.4 - - - +
317B TYR 3.2 0.2 - - - -
318B GLN* 1.3 75.6 - - - +
320B ILE* 1.3 64.8 + - - +
322B GLY 4.2 1.4 - - - -
323B MET* 3.7 22.5 + - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 5.5 1.3 - - + -
100B PRO* 3.8 29.4 - - + -
102B ILE* 4.5 20.0 - - + -
120B PHE* 3.7 40.8 - - + -
296B ILE* 4.9 3.8 - - + -
297B ALA* 6.1 0.4 - - - -
300B ALA* 3.7 16.4 - - + -
316B VAL* 2.9 25.9 + - + +
317B TYR* 3.1 5.4 + - - +
319B ALA* 1.3 77.7 - - - +
321B VAL* 1.3 58.3 + - - +
322B GLY 3.1 0.9 - - - -
323B MET* 3.0 34.1 + - + +
345B PHE* 3.6 19.6 - - + +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.1 11.4 - - + -
317B TYR* 3.0 60.3 + - + +
318B GLN* 3.7 19.3 - - - +
320B ILE* 1.3 74.7 - - - +
322B GLY* 1.3 56.1 + - - +
323B MET 3.4 1.8 - - - -
324B ASN* 3.0 14.9 + - - -
345B PHE 3.3 8.8 - - - +
346B THR* 3.5 13.7 - - - +
347B LYS* 3.7 34.7 + - + +
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG* 4.7 1.6 - - - -
307B ARG* 5.5 8.1 + - - -
318B GLN 3.3 15.7 + - - -
319B ALA* 4.2 2.7 - - - -
320B ILE 3.1 0.8 - - - -
321B VAL* 1.3 76.4 - - - +
323B MET* 1.3 54.7 + - - +
324B ASN* 2.9 22.0 + - - +
327B ASN* 3.5 17.5 - - - +
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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