Contacts of the helix formed by residues 321 - 338 (chain A) in PDB entry 3GIA
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 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASN* 4.7 4.3 + - - +
141A PHE* 3.9 26.3 - - + -
317A TRP* 3.8 16.7 + - + -
319A LYS 3.7 0.6 - - - -
320A SER* 1.3 72.8 + - - +
322A GLU* 1.3 64.2 + - - +
324A LEU* 3.0 22.9 + - + +
325A TYR* 3.5 25.8 - - + +
805A D10 4.7 11.0 - - + -
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 2.6 24.1 + - - +
304A LYS* 2.7 28.8 + - - -
320A SER* 3.3 19.5 - - - -
321A THR* 1.3 77.6 + - - +
323A GLY* 1.3 63.7 + - - +
325A TYR* 3.2 9.1 + - - +
326A ILE* 3.0 35.7 + - + +
800A D10 3.6 28.1 - - + +
805A D10 3.9 35.8 - - + +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.3 36.2 - - - -
317A TRP* 3.3 9.0 - - - -
320A SER 3.0 8.4 + - - -
322A GLU* 1.3 82.5 - - - +
324A LEU* 1.3 53.8 + - - +
326A ILE* 3.8 2.5 - - - +
327A THR* 2.8 37.9 + - - -
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Residues in contact with LEU 324 (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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137A THR* 3.7 26.2 - - + +
140A ASN* 3.6 38.1 - - + +
141A PHE* 4.2 12.1 - - + -
292A ILE* 4.1 9.4 - - + -
293A TYR* 3.9 16.4 - - + +
317A TRP* 3.4 42.7 - - + -
321A THR* 3.0 15.4 + - + +
323A GLY* 1.3 76.6 - - - +
325A TYR* 1.3 60.2 + - + +
327A THR* 3.7 1.8 - - - -
328A SER* 3.1 35.2 + - - +
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Residues in contact with TYR 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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137A THR* 4.0 24.7 - - + -
141A PHE* 3.1 34.9 - + - -
321A THR* 3.5 30.0 - - + +
322A GLU* 3.2 4.6 + - - +
324A LEU* 1.3 75.3 - - + +
326A ILE* 1.3 60.6 + - - +
328A SER* 3.9 4.5 - - - -
329A ALA* 2.9 32.2 + - - +
805A D10 3.7 59.7 - - + +
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Residues in contact with ILE 326 (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* 3.7 25.8 - - + -
300A TYR* 4.0 21.3 - - + +
322A GLU* 3.0 27.1 + - + +
323A GLY* 3.8 5.4 - - - +
324A LEU 3.3 0.2 - - - -
325A TYR* 1.3 72.5 - - - +
327A THR* 1.3 65.7 + - - +
329A ALA* 3.4 4.5 + - - +
330A LEU* 3.0 33.6 + - + +
800A D10 4.5 11.4 - - + -
805A D10 3.8 21.5 - - + -
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Residues in contact with THR 327 (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* 2.8 28.3 + - - -
98A VAL* 4.0 16.0 - - + +
101A ILE* 3.5 31.6 - - + +
292A ILE* 5.5 2.5 - - + -
296A ALA* 3.9 16.2 - - + -
317A TRP* 3.4 13.4 - - + -
323A GLY 2.8 24.3 + - - -
324A LEU* 3.7 5.4 - - + -
326A ILE* 1.3 77.3 - - - +
328A SER* 1.3 56.7 + - - +
331A GLY* 3.0 24.6 + - - -
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Residues in contact with SER 328 (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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101A ILE* 5.5 3.1 - - - +
133A VAL* 3.7 17.1 - - - +
137A THR* 2.5 33.7 + - - -
292A ILE* 5.6 5.2 - - - +
324A LEU* 3.1 21.7 + - - +
325A TYR* 3.9 5.6 - - - -
326A ILE 3.3 0.2 - - - -
327A THR* 1.3 75.2 - - - +
329A ALA* 1.3 60.1 + - - +
331A GLY* 3.3 2.1 + - - -
332A VAL* 3.0 34.5 + - - +
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Residues in contact with ALA 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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325A TYR 2.9 18.4 + - - +
326A ILE* 3.9 3.4 - - - +
328A SER* 1.3 76.5 - - - +
330A LEU* 1.3 57.3 + - - +
332A VAL* 3.3 7.3 + - - +
333A LEU* 2.9 27.8 + - - +
805A D10 4.5 16.4 - - + -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 3.7 30.5 - - + -
95A MET* 4.0 19.7 - - + -
98A VAL* 3.6 13.9 - - + -
326A ILE* 3.0 22.9 + - + +
329A ALA* 1.3 71.7 - - - +
331A GLY* 1.3 65.3 + - - +
333A LEU* 3.3 25.8 + - + +
334A PHE* 3.1 42.1 + - + -
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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
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98A VAL* 3.6 23.7 - - - +
101A ILE* 4.6 8.3 - - - -
102A ALA* 3.1 31.2 - - - +
133A VAL* 5.5 1.3 - - - -
327A THR 3.0 15.6 + - - -
328A SER 3.7 3.6 - - - -
329A ALA 3.3 0.2 - - - -
330A LEU* 1.3 76.5 - - - +
332A VAL* 1.3 61.4 + - - +
334A PHE* 4.9 0.2 - - - -
335A ALA* 3.2 7.3 + - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 4.7 2.2 - - + +
130A ILE* 3.7 38.4 - - + +
133A VAL* 3.9 29.4 - - + -
328A SER 3.0 21.1 + - - +
329A ALA* 3.7 6.1 - - - +
331A GLY* 1.3 71.7 - - - +
333A LEU* 1.3 65.5 + - - +
335A ALA* 3.2 8.1 + - + +
336A LEU* 2.9 45.1 + - + +
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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
----------------------------------------------------------
329A ALA 2.9 14.6 + - - +
330A LEU* 3.4 29.8 - - + +
332A VAL* 1.3 75.6 - - - +
334A PHE* 1.3 66.4 + - + +
336A LEU* 3.2 12.7 + - + +
337A LEU* 3.0 52.9 + - + +
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Residues in contact with PHE 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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95A MET* 3.6 31.9 - - + -
98A VAL* 4.5 4.0 - - + -
99A ILE* 4.0 31.4 - - + -
102A ALA* 3.8 17.3 - - + -
330A LEU* 3.1 39.1 + - + +
333A LEU* 1.3 82.8 - - + +
335A ALA* 1.3 62.0 + - - +
337A LEU* 4.7 1.3 - - + -
338A PHE* 3.2 57.8 + + - +
343A VAL* 3.8 5.0 - - + +
346A ILE* 4.2 12.6 - - + -
404A GLY 5.6 0.4 - - - -
408A THR* 4.1 20.2 - - + -
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Residues in contact with ALA 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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102A ALA* 3.7 23.3 - - + +
105A ALA* 5.0 2.5 - - + -
106A LYS* 2.8 36.5 + - + +
129A GLU* 3.7 28.5 - - + +
331A GLY 3.2 14.1 + - - +
332A VAL* 3.6 12.1 - - + +
333A LEU 3.2 0.4 - - - -
334A PHE* 1.3 76.9 - - - +
336A LEU* 1.3 58.0 + - + +
338A PHE 3.2 4.7 - - - +
343A VAL* 4.6 0.7 - - - -
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Residues in contact with LEU 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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126A ALA* 3.7 35.9 - - + +
129A GLU* 4.0 11.7 - - + +
130A ILE* 4.6 8.3 - - + -
332A VAL* 2.9 40.3 + - + +
333A LEU* 3.7 10.5 - - + +
335A ALA* 1.3 77.0 - - + +
337A LEU* 1.3 64.5 + - + +
338A PHE 3.5 0.9 - - - +
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Residues in contact with LEU 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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333A LEU* 3.0 42.9 + - + +
334A PHE* 5.2 1.1 - - + -
336A LEU* 1.3 80.9 - - + +
338A PHE* 1.3 89.8 + - + +
400A PHE* 3.6 30.8 - - + -
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Residues in contact with PHE 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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106A LYS* 2.8 30.0 + - - -
334A PHE* 3.2 38.2 + + - +
335A ALA 3.2 4.7 - - - +
336A LEU 4.6 1.1 - - - +
337A LEU* 1.3 99.8 - - + +
339A ASN* 1.3 56.1 + - - +
342A GLY* 4.2 2.0 - - - -
343A VAL* 3.8 17.0 - - + +
346A ILE* 3.7 31.6 - - + -
400A PHE* 3.7 45.8 - + - -
401A VAL* 4.1 19.3 - - + -
404A GLY* 4.3 13.5 - - - -
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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