Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 3LRB
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 PRO 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PRO* 6.2 0.2 - - + -
298A GLY* 4.5 8.7 - - - +
299A GLN* 5.8 4.5 - - - +
302A LYS* 3.6 28.9 - - + -
315A ALA 3.4 23.8 - - - +
317A VAL* 4.0 8.3 - - + -
322A THR* 1.3 86.0 - - + +
324A VAL* 1.3 69.5 + - - +
325A ALA 3.0 2.9 - - - -
326A GLY 2.5 16.4 + - - +
327A LEU* 3.1 38.3 - - + +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.2 35.9 - - + +
318A ASN* 3.8 46.1 - - + +
322A THR* 3.7 8.4 + - - +
323A PRO* 1.3 72.8 - - - +
325A ALA* 1.3 69.3 + - + +
327A LEU* 3.8 0.4 + - - -
328A ILE* 3.2 38.7 + - + +
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Residues in contact with ALA 325 (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 ILE* 5.5 2.0 - - + -
314A PHE* 4.8 7.0 - - + +
315A ALA 4.2 2.0 - - - +
316A ARG* 3.9 31.1 - - + +
317A VAL 5.3 0.4 - - - +
323A PRO 2.7 3.6 + - - -
324A VAL* 1.3 84.5 - - + +
326A GLY* 1.3 55.4 + - - +
328A ILE* 3.5 6.6 + - - +
329A ILE* 2.7 40.8 + - + +
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Residues in contact with GLY 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS* 3.4 30.0 + - - -
314A PHE* 3.8 13.5 - - - +
323A PRO* 2.5 17.1 + - - +
325A ALA* 1.3 72.9 - - - +
327A LEU* 1.3 53.3 + - - -
329A ILE* 2.6 29.1 + - - +
330A VAL* 3.1 10.7 + - - +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.8 26.8 - - + +
140A ASN* 2.9 49.4 - - + +
141A ILE* 4.3 6.3 - - + +
294A THR* 4.7 14.6 - - - +
295A LEU* 5.4 3.1 - - + -
298A GLY* 4.7 11.9 - - - -
302A LYS* 4.5 0.2 - - - +
322A THR* 5.6 0.9 - - + -
323A PRO* 3.1 48.2 + - + +
324A VAL* 4.6 1.1 - - - +
326A GLY* 1.3 71.7 - - - +
328A ILE* 1.3 58.4 + - - +
330A VAL* 3.1 14.5 + - + +
331A GLY 2.8 23.7 + - - -
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 3.7 15.5 - - + -
137A VAL* 4.2 4.7 - - - +
138A LEU* 5.9 1.3 - - + -
141A ILE* 3.9 20.8 - - + +
324A VAL* 3.2 37.4 + - + +
325A ALA* 3.7 7.4 - - - +
326A GLY 3.0 0.6 + - - -
327A LEU* 1.3 77.4 - - - +
329A ILE* 1.3 58.7 + - + +
331A GLY* 3.3 1.6 + - - -
332A ILE* 3.1 38.0 + - + +
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Residues in contact with ILE 329 (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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94A TRP* 5.9 5.6 - - + -
313A ILE* 4.3 24.5 - - + -
314A PHE* 4.7 16.2 - - + -
325A ALA* 2.7 30.7 - - + +
326A GLY* 2.6 14.7 + - - +
328A ILE* 1.3 72.6 - - + +
330A VAL* 1.3 59.1 + - - +
331A GLY 3.1 1.1 - - - -
332A ILE* 4.2 14.4 - - + -
333A LEU* 3.0 42.9 + - + +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 4.1 28.3 - - + +
98A TRP* 3.9 26.9 - - + -
137A VAL* 5.3 0.9 - - + -
294A THR* 5.2 11.0 - - - +
297A ALA* 4.6 13.2 - - + +
298A GLY 5.4 0.9 - - - +
302A LYS* 4.1 7.6 - - - +
326A GLY 3.1 11.6 + - - +
327A LEU* 3.4 14.8 - - + +
329A ILE* 1.3 77.2 - - + +
331A GLY* 1.3 50.5 + - - +
333A LEU* 4.3 4.7 - - - -
334A MET* 2.6 60.2 + - + +
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Residues in contact with GLY 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 3.2 27.6 - - - -
137A VAL* 4.0 12.8 - - - +
327A LEU 2.8 12.7 + - - -
328A ILE 3.3 0.4 + - - -
329A ILE 3.1 0.6 - - - -
330A VAL* 1.3 74.2 - - - +
332A ILE* 1.3 67.3 + - - +
334A MET* 3.7 4.1 - - - +
335A THR* 2.8 28.4 + - - -
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 3.3 12.4 - - + -
328A ILE* 3.1 28.2 + - + +
329A ILE* 4.0 20.0 - - + +
331A GLY* 1.3 73.8 - - - +
333A LEU* 1.3 65.1 + - + +
335A THR* 3.3 5.0 - - - -
336A ILE* 3.0 42.0 + - + +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 5.2 7.4 - - + -
98A TRP* 3.3 45.3 - - + +
329A ILE* 3.0 27.9 + - + +
330A VAL* 3.9 5.2 - - - +
332A ILE* 1.3 77.9 - - + +
334A MET* 1.3 68.6 + - - +
336A ILE* 3.0 29.5 + - + +
337A PHE* 3.3 12.1 + - + +
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Residues in contact with MET 334 (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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98A TRP* 4.1 15.6 - - + +
101A ASN* 3.8 33.2 - - + -
102A ILE* 3.3 26.7 - - + +
133A LEU* 3.6 32.8 - - + +
137A VAL* 3.8 22.2 - - + -
294A THR* 4.7 6.1 - - + -
330A VAL* 2.6 58.5 + - + +
331A GLY* 3.7 3.6 - - - +
333A LEU* 1.3 73.0 - - - +
335A THR* 1.3 66.6 + - - +
338A GLN* 2.9 20.0 + - - +
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Residues in contact with THR 335 (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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130A VAL* 3.4 15.7 - - + +
133A LEU* 4.4 5.0 - - - +
134A TRP* 3.1 23.8 + - - +
331A GLY 2.8 18.4 + - - -
332A ILE* 3.3 9.4 - - - -
333A LEU 3.0 0.4 + - - -
334A MET* 1.3 74.5 - - - +
336A ILE* 1.3 60.5 + - + +
337A PHE 3.0 0.3 - - - -
338A GLN* 2.4 40.2 + - - +
339A LEU* 3.0 33.5 + - + -
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Residues in contact with ILE 336 (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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332A ILE* 3.0 39.7 - - + +
333A LEU* 3.0 23.4 + - + +
335A THR* 1.3 77.9 - - + +
337A PHE* 1.3 61.1 + - - +
339A LEU* 3.8 13.9 + - + +
340A SER* 3.1 19.2 + - - +
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Residues in contact with PHE 337 (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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98A TRP* 5.1 4.5 - - + +
99A ILE* 4.9 15.9 - - + -
102A ILE* 3.0 51.1 - - + -
103A ALA* 5.7 3.1 - - + -
333A LEU* 3.3 8.3 + - + +
334A MET 4.1 0.2 - - - +
335A THR 2.7 4.8 + - - -
336A ILE* 1.3 72.9 - - - +
338A GLN* 1.3 54.2 + - - +
339A LEU 2.6 14.6 + - - -
340A SER* 2.7 24.4 + - - -
341A SER* 3.0 19.4 + - - -
345A ASN* 2.8 35.2 - - - -
353A VAL* 4.2 22.4 - - + -
354A SER* 5.8 1.8 - - - -
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Residues in contact with GLN 338 (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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102A ILE* 3.6 27.3 + - + +
105A VAL* 3.4 9.9 - - - +
106A VAL* 3.9 9.7 - - - +
126A THR* 4.7 6.1 + - - +
129A CYS* 2.8 48.9 - - - +
130A VAL* 4.1 14.5 - - + +
133A LEU* 3.3 24.2 - - + -
334A MET 2.9 11.9 + - - +
335A THR* 2.4 26.8 + - - +
337A PHE* 1.3 70.4 - - - +
339A LEU* 1.3 55.4 + - - +
340A SER 3.5 2.3 + - - -
341A SER 3.6 15.8 - - - +
342A ILE* 3.6 4.7 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 4.2 6.3 - - - +
127A ILE* 5.8 7.0 - - + -
130A VAL* 3.4 20.2 - - + -
335A THR* 3.4 32.8 - - + +
336A ILE* 3.9 11.0 - - + +
337A PHE 2.6 4.4 + - - -
338A GLN* 1.3 72.3 - - - +
340A SER* 1.3 66.5 + - - +
342A ILE* 3.3 29.2 - - + +
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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