Contacts of the helix formed by residues 425 - 443 (chain B) in PDB entry 3N9Y
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 425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B CYS* 3.2 10.5 - - - -
424B LEU* 1.3 77.5 - - - +
426B ARG* 1.3 57.4 + - - +
427B ARG 3.3 2.5 - - - -
428B ILE* 3.2 10.5 + - - +
429B ALA* 2.8 31.6 + - - +
601B HEM 3.4 38.7 - - - +
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Residues in contact with ARG 426 (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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120B MET* 4.3 5.4 - - + -
413B ASN* 3.4 32.5 + - - +
416B PHE* 3.5 46.6 - - + +
417B GLY 4.2 10.7 + - - -
422B GLN* 2.9 31.6 - - - +
423B CYS* 3.3 21.7 - - + +
424B LEU 3.2 4.2 + - - -
425B GLY* 1.3 76.7 - - - +
427B ARG* 1.3 75.2 + - - +
429B ALA* 3.4 1.0 + - - +
430B GLU* 2.8 61.2 + - - +
76D ASP* 4.6 10.9 + - - +
77D MET* 3.5 18.1 - - - +
80D LEU* 5.8 2.6 - - - +
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL 3.9 3.8 - - - +
120B MET* 3.7 47.6 + - - +
122B PRO* 6.3 1.3 - - - -
125B THR* 3.9 25.4 - - + -
128B PHE* 5.3 0.2 - - - -
422B GLN* 5.0 2.6 - - - +
425B GLY 3.3 0.2 - - - -
426B ARG* 1.3 100.0 - - - +
428B ILE* 1.3 66.1 + - - +
430B GLU* 3.0 33.6 + - - -
431B LEU* 2.9 36.3 + - + +
50D LEU* 3.3 27.1 + - - +
73D GLU* 3.6 39.4 + - - +
76D ASP* 5.7 2.8 + - - +
77D MET* 5.2 5.7 - - - +
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Residues in contact with ILE 428 (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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119B VAL* 4.3 15.2 + - + +
128B PHE* 3.5 29.6 - - + -
132B LEU* 4.2 8.5 - - + +
171B ILE* 4.0 25.8 - - + -
174B VAL* 4.4 10.5 - - + -
262B ILE* 4.1 14.8 - - + -
284B MET* 3.9 28.0 - - + -
425B GLY* 3.2 8.2 + - - +
427B ARG* 1.3 77.1 - - - +
429B ALA* 1.3 53.1 + - - +
431B LEU* 3.8 2.0 - - - +
432B GLU* 2.8 49.9 + - - +
601B HEM 4.3 11.4 - - + -
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Residues in contact with ALA 429 (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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292B THR* 3.7 26.5 - - + -
416B PHE* 4.0 10.3 - - + -
425B GLY 2.8 20.4 + - - +
426B ARG 3.7 3.1 - - - +
428B ILE* 1.3 72.5 - - - +
430B GLU* 1.3 63.9 + - - +
432B GLU* 3.7 0.8 - - - +
433B MET* 3.0 33.0 + - - +
601B HEM 3.9 27.1 - - + -
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Residues in contact with GLU 430 (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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342B ILE* 4.6 6.5 - - + +
416B PHE* 4.1 16.0 - - + -
426B ARG* 2.8 57.1 + - + +
427B ARG* 3.0 33.5 + - - +
429B ALA* 1.3 71.9 - - - +
431B LEU* 1.3 58.9 + - + +
433B MET* 4.0 7.1 - - + +
434B THR* 2.6 40.1 + - - +
73D GLU* 3.8 9.0 - - - +
76D ASP* 4.7 7.9 - - - +
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Residues in contact with LEU 431 (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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125B THR* 3.9 31.6 - - - +
128B PHE* 4.3 10.5 - - + -
129B LEU* 3.6 30.7 - - + -
132B LEU* 3.8 14.6 - - + -
332B LEU* 4.1 18.4 - - + -
339B LYS* 6.0 3.6 - - - +
427B ARG* 2.9 23.8 + - + +
430B GLU* 1.3 78.1 - - + +
432B GLU* 1.3 64.6 + - - +
434B THR* 4.7 2.2 - - - -
435B ILE* 2.9 33.1 + - + +
73D GLU* 5.9 2.9 - - - +
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Residues in contact with GLU 432 (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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132B LEU* 3.7 17.6 - - + +
136B SER* 4.4 0.7 + - - -
166B PHE* 3.4 29.9 - - + -
167B ALA* 3.7 11.2 - - - +
170B SER* 3.6 25.7 - - - +
171B ILE* 4.6 4.0 + - - +
288B GLY 5.0 1.9 - - - +
292B THR* 2.8 37.3 + - + +
428B ILE* 2.8 35.0 + - - +
429B ALA 3.7 3.8 - - - +
431B LEU* 1.3 73.5 - - - +
433B MET* 1.3 57.7 + - + +
435B ILE* 4.1 1.0 - - - +
436B PHE* 3.0 30.7 + - - +
601B HEM 5.3 1.7 - - - +
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Residues in contact with MET 433 (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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292B THR* 4.2 15.7 - - - +
295B THR* 3.6 33.9 - - + -
296B LEU* 3.8 29.2 - - + -
342B ILE* 4.0 34.3 - - + -
346B LEU* 4.9 0.7 - - + -
416B PHE* 4.1 9.4 - - + -
429B ALA 3.0 29.0 + - - +
430B GLU* 4.0 4.0 - - - +
432B GLU* 1.3 73.3 - - - +
434B THR* 1.3 66.0 + - - +
436B PHE* 3.5 0.9 + - - +
437B LEU* 3.0 31.1 + - + +
601B HEM 3.8 23.1 - - + -
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Residues in contact with THR 434 (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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332B LEU* 3.6 25.8 - - + -
335B VAL* 4.3 12.1 - - + -
338B LEU* 3.9 24.5 - - + +
339B LYS* 4.5 18.3 - - + +
342B ILE* 3.4 16.6 - - + +
430B GLU* 2.6 25.7 + - - +
431B LEU* 3.4 2.4 + - - -
433B MET* 1.3 74.8 - - - +
435B ILE* 1.3 58.4 + - - +
437B LEU* 3.4 0.7 + - - -
438B ILE* 3.0 34.0 + - + +
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Residues in contact with ILE 435 (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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129B LEU* 4.1 33.9 - - + +
132B LEU* 4.1 20.0 - - + -
133B ASP* 3.6 38.8 - - + +
136B SER* 4.2 5.2 - - - +
328B MET* 4.0 20.6 - - + -
332B LEU* 4.1 12.6 - - + -
431B LEU* 2.9 24.3 + - + +
432B GLU* 4.2 2.9 - - - +
434B THR* 1.3 71.9 - - - +
436B PHE* 1.3 66.2 + - - +
438B ILE* 3.5 7.6 + - - +
439B ASN* 2.8 33.6 + - - +
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Residues in contact with PHE 436 (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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136B SER* 3.2 17.2 + - - +
139B PHE* 3.6 39.3 - + + -
163B LEU* 3.9 20.9 - - + -
166B PHE* 3.5 29.6 - + + -
296B LEU* 3.5 30.1 - - + -
300B LEU* 4.3 15.0 - - + -
432B GLU 3.0 22.0 + - - +
433B MET 3.7 2.7 - - - +
435B ILE* 1.3 76.0 - - - +
437B LEU* 1.3 71.6 + - + +
439B ASN* 3.3 4.2 + - - +
440B MET* 2.9 56.4 + - + +
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Residues in contact with LEU 437 (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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296B LEU* 3.8 15.3 - - + -
299B HIS* 3.6 52.0 - - + +
300B LEU* 4.4 14.1 - - + -
303B MET* 4.5 4.3 - - + -
338B LEU* 4.0 20.9 - - + -
342B ILE* 4.1 13.9 - - + -
433B MET* 3.0 20.5 + - + +
434B THR 4.0 1.6 - - - +
435B ILE 3.3 0.2 - - - -
436B PHE* 1.3 93.4 - - + +
438B ILE* 1.3 61.3 + - - +
440B MET* 4.0 3.8 - - + +
441B LEU* 2.9 38.8 + - + +
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Residues in contact with ILE 438 (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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317B VAL* 3.8 17.2 - - + +
321B ARG* 3.8 9.2 - - - +
328B MET* 4.0 18.2 - - + -
331B MET* 3.3 35.4 - - + -
332B LEU* 4.0 25.6 - - + -
335B VAL* 4.7 9.2 - - + -
338B LEU* 3.7 14.4 - - + -
434B THR* 3.0 25.3 + - + +
435B ILE* 3.7 4.9 - - - +
437B LEU* 1.3 76.0 - - - +
439B ASN* 1.3 62.6 + - - +
442B GLU* 3.2 41.2 + - - +
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Residues in contact with ASN 439 (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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133B ASP* 3.1 23.3 + - - +
136B SER* 3.6 18.1 - - - -
137B ARG* 3.5 25.1 + - - +
140B VAL* 3.7 17.3 - - + +
321B ARG* 4.4 8.9 + - - -
328B MET* 4.5 5.7 - - - +
435B ILE* 2.8 26.1 + - - +
436B PHE 3.3 6.9 + - - +
438B ILE* 1.3 80.8 - - - +
440B MET* 1.3 61.2 + - - +
442B GLU* 4.0 7.8 - - - +
443B ASN* 2.9 34.3 + - - +
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Residues in contact with MET 440 (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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139B PHE* 4.0 17.9 - - + -
140B VAL* 4.4 5.8 - - + -
143B LEU* 3.5 33.0 - - + -
300B LEU* 4.5 16.2 - - + -
303B MET* 6.0 1.1 - - + -
436B PHE* 2.9 48.2 + - + +
437B LEU* 4.0 7.4 - - + +
438B ILE 3.4 0.2 - - - -
439B ASN* 1.3 76.9 - - - +
441B LEU* 1.3 58.6 + - + +
443B ASN 3.2 0.2 + - - -
444B PHE* 2.8 53.7 + - + +
472B PHE* 3.5 24.2 - - + -
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Residues in contact with LEU 441 (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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303B MET* 3.7 33.9 - - + -
310B GLN* 4.1 15.5 - - + +
313B LEU* 3.7 32.3 - - + +
314B ARG* 2.9 62.7 + - + +
317B VAL* 4.1 15.0 - - + -
338B LEU* 4.2 13.5 - - + -
437B LEU* 2.9 25.7 + - + +
438B ILE 4.1 2.5 - - - +
440B MET* 1.3 74.1 - - + +
442B GLU* 1.3 60.4 + - - +
443B ASN 3.4 0.3 + - - -
444B PHE 3.8 4.1 + - - +
475B PHE* 4.2 0.7 - - - -
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Residues in contact with GLU 442 (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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317B VAL* 3.6 13.6 - - + +
318B LEU* 4.2 20.6 - - + +
321B ARG* 2.7 61.3 + - - +
331B MET* 3.9 2.4 - - - +
438B ILE* 3.2 25.0 + - - +
439B ASN* 3.9 10.2 - - - +
441B LEU* 1.3 76.5 - - - +
443B ASN* 1.3 66.7 + - - +
475B PHE* 3.5 20.2 - - - +
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Residues in contact with ASN 443 (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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140B VAL* 3.5 19.2 - - - +
144B HIS* 3.0 24.0 + - - +
439B ASN* 2.9 28.9 + - - +
440B MET 3.2 1.8 + - - -
442B GLU* 1.3 91.4 + - - +
444B PHE* 1.3 88.1 + - + +
474B PRO* 3.4 2.8 - - - +
475B PHE* 2.8 24.9 + - - +
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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
------------------------------------------------------------
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