Contacts of the helix formed by residues 443 - 461 (chain A) in PDB entry 2IAG
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 GLY 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 4.0 9.4 - - - -
441A CYS* 3.3 9.0 - - - -
442A LEU* 1.3 79.0 - - - +
444A ARG* 1.3 52.3 + - - +
445A SER 3.5 1.6 - - - -
446A TYR* 3.1 10.1 + - - +
447A ALA* 2.8 33.3 + - - +
600A HEM 3.4 32.4 - - - +
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Residues in contact with ARG 444 (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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431A ASN 5.7 2.4 + - - -
434A TRP* 3.1 71.1 - - + +
440A HIS* 5.8 6.3 - - - +
441A CYS* 3.4 20.7 - - + +
442A LEU 3.5 3.0 + - - -
443A GLY* 1.3 75.2 - - - +
445A SER* 1.3 60.9 + - - +
447A ALA* 3.2 2.1 + - - +
448A VAL* 2.9 38.1 + - + +
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Residues in contact with SER 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 5.2 1.1 - - - -
129A LEU* 4.4 15.6 - - - +
133A LEU* 3.6 25.1 - - - +
443A GLY 3.5 0.4 - - - -
444A ARG* 1.3 81.0 - - - +
446A TYR* 1.3 57.6 + - - +
448A VAL* 3.8 5.2 - - - +
449A ASN* 2.9 39.7 + - - +
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Residues in contact with TYR 446 (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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128A LEU* 5.0 6.7 + - + +
133A LEU* 3.6 21.4 - - + +
136A LEU* 4.2 33.4 - - + -
137A THR* 4.9 2.9 - - - -
140A MET* 3.3 36.3 - - + -
176A GLY* 3.7 15.9 + - - -
179A THR* 4.0 9.9 - - + -
180A LEU* 4.4 9.6 - - + +
285A GLN* 5.1 0.4 - - - -
288A MET* 4.6 5.6 - - + +
443A GLY* 3.1 10.4 + - - +
445A SER* 1.3 79.1 - - - +
447A ALA* 1.3 54.6 + - - +
449A ASN* 3.8 3.7 - - + +
450A SER* 2.7 54.4 + - - -
600A HEM 3.2 48.7 - - + -
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Residues in contact with ALA 447 (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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288A MET* 4.1 5.8 - - + +
434A TRP* 4.0 7.6 - - + -
443A GLY 2.8 15.6 + - - +
444A ARG 3.5 4.5 - - - +
446A TYR* 1.3 72.0 - - - +
448A VAL* 1.3 58.8 + - - +
450A SER* 3.5 1.0 + - - -
451A ILE* 3.0 36.9 + - - +
600A HEM 3.5 55.4 - - + -
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASP* 4.9 2.2 - - - +
345A LEU* 3.8 26.9 - - + +
434A TRP* 3.7 25.4 - - + -
444A ARG* 2.9 26.1 + - + +
445A SER* 3.8 6.3 - - - +
447A ALA* 1.3 73.5 - - - +
449A ASN* 1.3 70.9 + - - +
451A ILE* 3.3 3.6 + - - +
452A LYS* 3.0 48.9 + - + +
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Residues in contact with ASN 449 (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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133A LEU* 4.2 11.4 - - - +
137A THR* 3.4 34.2 + - + +
335A LEU* 3.8 32.7 + - + +
445A SER* 2.9 25.0 + - - +
446A TYR* 3.8 4.9 - - + +
448A VAL* 1.3 83.4 - - - +
450A SER* 1.3 58.1 - - - +
452A LYS* 3.4 4.1 + - - +
453A GLN* 2.9 34.8 + - - +
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Residues in contact with SER 450 (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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140A MET* 3.3 25.5 - - - +
144A LEU* 3.8 3.6 - - - +
172A LEU* 3.9 7.0 - - - +
288A MET* 3.5 23.6 - - - -
446A TYR* 2.7 35.3 + - - -
447A ALA 3.7 0.4 - - - -
449A ASN* 1.3 73.5 - - - +
451A ILE* 1.3 66.4 + - - +
453A GLN* 3.3 12.2 + - - +
454A PHE* 3.0 24.3 + - - +
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Residues in contact with ILE 451 (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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172A LEU* 4.8 6.5 - - + -
288A MET* 4.2 22.9 - - + +
291A ALA* 3.9 16.6 - - + -
292A ALA* 4.8 9.2 - - + -
295A LEU* 4.2 15.3 - - + -
341A LEU* 6.1 0.9 - - + -
345A LEU* 4.0 30.7 - - + -
434A TRP* 5.7 0.7 - - + -
447A ALA 3.0 23.2 + - - +
448A VAL* 3.8 4.5 - - - +
450A SER* 1.3 74.7 - - - +
452A LYS* 1.3 58.8 + - + +
454A PHE* 3.2 7.1 + - - +
455A VAL* 2.9 38.3 + - + +
600A HEM 3.9 28.0 - - + -
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Residues in contact with LYS 452 (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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334A VAL* 3.9 15.5 - - + +
335A LEU* 2.9 32.3 + - + +
336A ASP* 5.1 0.2 - - - +
338A THR* 2.7 23.4 + - - +
341A LEU* 3.8 29.6 - - + +
342A ASP* 2.6 36.6 + - - +
345A LEU* 5.2 7.0 - - + -
448A VAL* 3.0 37.9 + - + +
449A ASN* 3.7 6.5 - - - +
451A ILE* 1.3 78.9 - - + +
453A GLN* 1.3 55.9 + - - +
455A VAL* 3.9 2.8 - - - +
456A PHE* 2.9 31.1 + - - +
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Residues in contact with GLN 453 (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* 3.0 36.4 + - - +
140A MET* 3.5 34.6 - - - +
141A TYR* 3.4 31.8 - - + +
144A LEU* 3.7 9.6 - - + +
330A LEU* 4.4 9.1 - - + +
334A VAL* 5.4 0.4 - - - -
335A LEU* 4.0 15.2 - - + +
449A ASN* 2.9 23.2 + - - +
450A SER* 3.6 7.6 + - - +
452A LYS* 1.3 76.5 - - - +
454A PHE* 1.3 57.2 + - - +
456A PHE* 3.5 6.6 + - - +
457A LEU* 2.9 33.3 + - - +
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Residues in contact with PHE 454 (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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144A LEU* 3.7 23.9 - - + +
148A LEU* 4.7 9.4 - - + -
167A PHE* 3.6 25.8 - + - -
168A SER* 3.9 30.3 - - - -
171A PHE* 3.7 23.3 - + + -
172A LEU* 3.6 29.2 - - + -
292A ALA* 4.0 8.3 - - + -
296A LEU* 3.9 20.6 - - + -
450A SER 3.0 17.1 + - - +
451A ILE 3.6 3.6 - - - +
453A GLN* 1.3 74.7 - - - +
455A VAL* 1.3 62.4 + - + +
457A LEU* 3.2 6.1 + - + +
458A VAL* 2.9 45.8 + - + +
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Residues in contact with VAL 455 (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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292A ALA* 5.5 2.7 - - + -
295A LEU* 4.0 25.8 - - + -
296A LEU* 4.6 14.8 - - + -
299A LEU* 4.9 0.4 - - + -
309A VAL* 4.5 4.5 - - + -
313A LEU* 4.6 3.4 - - + -
341A LEU* 4.3 20.2 - - + -
451A ILE* 2.9 34.9 + - + +
452A LYS* 3.9 5.6 - - - +
454A PHE* 1.3 77.9 - - + +
456A PHE* 1.3 57.9 + - - +
458A VAL* 3.3 6.0 + - - +
459A LEU* 2.9 53.6 + - + +
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Residues in contact with PHE 456 (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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141A TYR* 3.9 13.2 - - - -
313A LEU* 4.1 25.7 - - + +
317A LEU* 4.3 25.4 - - + -
330A LEU* 3.5 25.4 - - + -
331A PRO* 4.4 9.2 - - + -
334A VAL* 3.6 37.0 - - + -
452A LYS 2.9 19.6 + - - +
453A GLN* 3.6 6.1 - - - +
455A VAL* 1.3 77.7 - - - +
457A LEU* 1.3 72.1 + - + +
459A LEU 4.0 0.2 - - - -
460A VAL* 3.1 58.9 + - + +
461A HIS* 4.9 4.3 - + - -
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Residues in contact with LEU 457 (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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141A TYR* 3.7 32.3 - - + +
144A LEU* 3.8 21.1 - - + +
145A HIS* 3.8 39.9 - - + +
148A LEU* 4.2 18.3 - - + +
149A LEU* 5.4 0.9 - - + -
453A GLN 2.9 22.0 + - - +
454A PHE* 3.2 6.2 + - + +
456A PHE* 1.3 78.2 - - + +
458A VAL* 1.3 56.6 + - - +
461A HIS* 3.0 63.3 + - + +
462A LEU* 4.0 1.2 + - - +
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Residues in contact with VAL 458 (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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148A LEU* 4.9 2.5 - - + -
167A PHE* 3.8 28.0 - - + -
296A LEU* 4.5 5.8 - - + -
454A PHE* 2.9 39.8 + - + +
455A VAL* 3.9 5.6 - - - +
457A LEU* 1.3 75.4 - - - +
459A LEU* 1.3 69.4 + - + +
462A LEU* 3.1 47.7 + - + +
464A LEU* 4.0 34.9 - - + +
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Residues in contact with LEU 459 (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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296A LEU* 4.2 16.4 - - + -
299A LEU* 4.5 2.7 - - + -
300A LEU* 6.4 2.0 - - + -
306A LEU* 3.9 25.1 - - + -
309A VAL* 3.5 33.4 - - + -
310A ARG* 3.0 44.8 + - + +
313A LEU* 4.2 11.0 - - + -
314A GLU* 5.4 2.3 - - - +
455A VAL* 2.9 29.6 + - + +
456A PHE 4.4 1.1 - - - +
458A VAL* 1.3 86.1 - - + +
460A VAL* 1.3 61.8 - - + +
462A LEU 4.2 1.7 - - - +
464A LEU* 5.7 3.8 - - + -
499A ARG* 5.5 0.5 + - - -
130B HIS* 4.0 8.7 + - - -
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Residues in contact with VAL 460 (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 LEU* 4.9 11.7 - - + +
314A GLU* 4.7 14.6 - - - +
317A LEU* 4.1 24.7 - - + -
456A PHE* 3.1 50.8 + - + +
457A LEU 4.6 0.2 - - - +
459A LEU* 1.3 85.0 - - + +
461A HIS* 1.3 72.4 + - + +
462A LEU 3.6 0.9 - - - -
499A ARG* 4.0 21.7 + - - +
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Residues in contact with HIS 461 (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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141A TYR* 4.8 5.2 - - - -
145A HIS* 4.5 6.4 + + - -
148A LEU* 5.4 0.2 - - + -
149A LEU* 3.9 32.3 - - + +
456A PHE* 4.9 4.5 - + - -
457A LEU* 3.0 47.3 + - + +
460A VAL* 1.3 89.6 - - + +
462A LEU* 1.3 68.8 + - + +
498A ILE* 3.6 10.7 - - + +
499A ARG* 2.8 26.1 + - - +
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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
------------------------------------------------------------
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