Contacts of the helix formed by residues 492 - 509 (chain C) in PDB entry 4C1M
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 492 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C GLY 4.7 7.8 + - - -
483C GLU* 3.7 12.8 + - - -
484C PRO 3.2 16.9 + - - -
485C LEU* 4.2 4.0 - - - +
486C LYS* 3.9 3.4 - - - -
491C VAL* 1.3 76.5 - - - +
493C PRO* 1.3 70.7 - - - +
494C LEU 3.4 3.1 + - - -
495C LEU* 3.5 2.6 + - - +
496C ALA* 3.0 27.2 + - - +
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Residues in contact with PRO 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C TYR* 4.8 1.7 + - - -
437C ARG* 4.2 11.4 - - - +
442C LEU* 3.9 23.5 - - + +
483C GLU* 3.3 15.7 - - + +
484C PRO* 4.0 11.0 - - + +
486C LYS* 4.0 27.6 - - + +
492C GLY* 1.3 85.3 - - - +
494C LEU* 1.3 60.2 + - - +
496C ALA* 3.6 2.1 - - + +
497C CYS* 3.0 24.4 + - - +
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C TYR* 3.5 35.4 - - + -
436C TRP* 3.4 39.0 - - + +
437C ARG* 3.7 9.9 - - + +
440C CYS* 3.5 15.0 - - + -
442C LEU* 3.7 9.3 - - + +
476C ILE* 3.7 24.9 - - + -
480C GLY* 4.5 9.9 - - - -
483C GLU* 2.9 25.1 + - - +
493C PRO* 1.3 73.3 - - - +
495C LEU* 1.3 63.6 + - + +
497C CYS* 3.3 3.9 + - - +
498C ILE* 3.2 22.5 + - + +
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Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ALA* 3.7 34.3 - - + +
334C TYR* 3.7 25.8 - - + -
476C ILE* 4.8 8.3 - - + +
477C TRP* 5.5 2.5 - - + +
480C GLY* 3.5 44.0 - - - +
481C VAL* 3.9 8.1 - - + +
483C GLU* 4.5 0.4 + - - -
491C VAL* 3.8 24.0 - - + -
492C GLY 3.5 3.1 + - - +
493C PRO 3.4 0.2 - - - -
494C LEU* 1.3 73.9 - - - +
496C ALA* 1.3 66.4 + - - +
498C ILE* 4.5 7.2 - - + +
499C ILE* 2.9 35.3 + - + +
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Residues in contact with ALA 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 3.5 10.0 - - + +
305C ALA* 3.8 16.8 - - + -
309C TYR* 4.0 7.9 - - + -
486C LYS* 3.8 20.9 - - + -
491C VAL* 3.7 15.1 - - + +
492C GLY 3.0 19.7 + - - +
493C PRO* 3.6 5.4 - - + +
494C LEU 3.3 0.2 - - - -
495C LEU* 1.3 74.7 - - - +
497C CYS* 1.3 57.0 + - - +
500C GLY* 2.8 29.8 + - - -
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Residues in contact with CYS 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C TYR* 3.4 34.7 - - - +
439C PHE* 5.1 2.2 - - - -
440C CYS* 3.1 47.3 - - + -
442C LEU* 5.2 0.7 - - + -
493C PRO 3.0 15.2 + - - +
494C LEU 3.8 0.2 - - - +
495C LEU 3.2 0.4 - - - -
496C ALA* 1.3 74.9 - - - +
498C ILE* 1.3 58.5 + - - +
501C THR* 2.7 46.5 + - - -
3F BMA 4.3 11.0 - - - -
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.9 16.5 - - + -
327C VAL* 3.7 41.7 - - + -
328C PHE* 4.2 9.6 - - + -
331C ALA* 3.7 26.9 - - + -
436C TRP* 4.6 10.3 - - + -
439C PHE* 5.4 2.0 - - + -
440C CYS* 4.2 12.8 - - - -
476C ILE* 3.9 21.3 - - + -
494C LEU* 3.2 24.5 + - + +
495C LEU* 3.3 4.9 + - + +
497C CYS* 1.3 74.7 - - - +
499C ILE* 1.3 62.7 + - - +
501C THR* 4.8 0.2 - - - -
502C GLN* 3.2 22.3 + - - +
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Residues in contact with ILE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 4.6 3.4 - - + -
300C VAL* 4.6 8.3 - - + -
301C LEU* 4.0 16.2 - - + -
328C PHE* 4.1 11.0 - - + -
331C ALA* 4.1 12.1 - - + +
332C PHE* 3.8 23.8 - - + +
334C TYR* 3.9 29.2 - - + -
491C VAL* 4.3 7.2 - - + -
495C LEU* 2.9 34.7 + - + +
498C ILE* 1.3 72.6 - - - +
500C GLY* 1.3 66.6 + - - +
502C GLN* 3.3 1.9 + - - +
503C PHE* 3.0 52.9 + - + -
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Residues in contact with GLY 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 3.9 17.4 - - - +
309C TYR* 3.7 23.3 - - - +
310C LEU* 4.2 4.6 - - - +
496C ALA 2.8 23.3 + - - -
499C ILE* 1.3 73.9 - - - +
501C THR* 1.3 61.0 + - - +
503C PHE* 3.3 1.8 + - - +
504C ARG* 3.0 22.7 + - - +
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Residues in contact with THR 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 4.0 19.7 - - + -
309C TYR* 4.0 12.5 - - - +
439C PHE* 5.5 1.5 - - + -
497C CYS* 2.7 35.1 + - - -
498C ILE* 4.1 2.9 - - - -
500C GLY* 1.3 75.1 - - - +
502C GLN* 1.3 60.5 + - - +
504C ARG* 3.3 8.1 + - + +
505C LYS* 3.2 26.3 + - + +
6E FUC 6.1 0.7 - - + +
3F BMA 4.4 8.1 - - - +
5F MAN 3.9 34.3 - - - +
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Residues in contact with GLN 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.9 11.9 - - + -
322C PRO 4.5 0.2 + - - -
323C ARG 2.9 24.0 + - - -
324C ILE* 3.4 22.9 - - + +
325C ALA* 2.9 29.6 + - - +
328C PHE* 3.4 45.8 - - + +
498C ILE 3.2 12.3 + - - +
499C ILE 3.3 3.1 + - - +
501C THR* 1.3 75.4 - - - +
503C PHE* 1.3 59.2 + - + +
505C LYS* 3.2 7.5 + - - +
506C LEU* 3.0 43.1 + - + +
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Residues in contact with PHE 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.7 26.5 - - + -
97A LEU* 3.6 32.1 - - + -
171C VAL* 4.5 4.7 - - + -
292C THR* 4.3 4.5 - - + -
293C TYR* 2.7 42.6 + + + +
297C LEU* 3.5 40.4 - - + -
301C LEU* 6.4 0.2 - - + -
310C LEU* 3.8 8.1 - - + -
328C PHE* 3.7 20.6 - + - -
332C PHE* 3.8 13.5 - + - -
499C ILE* 3.0 30.6 + - + +
500C GLY 4.1 2.7 - - - +
502C GLN* 1.3 73.4 - - - +
504C ARG* 1.3 63.4 + - - +
506C LEU* 4.0 10.8 - - + -
507C ARG* 3.1 9.4 + - - +
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Residues in contact with ARG 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C LYS 4.8 3.8 + - - -
309C TYR* 3.3 24.7 + - - +
310C LEU* 3.6 8.4 - - - +
311C PRO* 3.5 29.5 - - - +
500C GLY 3.0 8.0 + - - +
501C THR* 3.4 12.1 - - + +
502C GLN 3.2 0.4 - - - -
503C PHE* 1.3 78.5 - - - +
505C LYS* 1.3 52.3 + - + +
507C ARG* 3.4 17.7 + - - +
508C ASP* 2.6 59.4 + - - +
6E FUC 3.7 46.2 + - + +
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Residues in contact with LYS 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 4.1 24.8 - - + +
320C VAL* 3.6 11.6 - - + +
321C ASP* 3.4 36.8 + - - +
322C PRO* 3.9 7.5 - - - +
323C ARG 5.7 0.4 - - - +
501C THR* 3.2 15.4 + - + +
502C GLN* 3.2 14.2 + - - +
504C ARG* 1.3 74.9 - - - +
506C LEU* 1.3 58.4 + - - +
509C GLY* 2.8 30.3 + - - -
6E FUC 3.8 24.4 + - + -
5F MAN 3.0 45.8 + - - +
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Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.7 28.7 - - + -
169C SER* 3.4 21.5 - - - +
170C PHE* 4.5 4.9 - - - +
171C VAL* 4.2 12.1 + - + +
293C TYR* 3.7 12.6 - - - +
322C PRO* 3.1 31.9 - - + +
324C ILE* 3.9 17.9 - - + -
502C GLN* 3.0 28.1 + - + +
503C PHE* 4.0 19.1 - - + -
505C LYS* 1.3 77.4 - - - +
507C ARG* 1.3 55.6 + - - +
510C ASP* 3.1 27.0 - - - +
513C TRP* 4.8 2.2 - - - -
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Residues in contact with ARG 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C TYR* 3.7 22.0 + - + +
310C LEU* 3.8 24.2 + - - +
311C PRO* 2.7 32.8 + - - +
312C THR 4.5 1.0 + - - -
313C TYR* 3.7 36.2 - - + +
503C PHE 3.1 17.7 + - - +
504C ARG* 3.6 23.6 - - - +
506C LEU* 1.3 76.7 - - - +
508C ASP* 1.3 86.0 + - - +
509C GLY 3.3 0.7 + - - -
510C ASP* 3.4 17.3 + - - +
513C TRP* 3.5 47.6 - - + +
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Residues in contact with ASP 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C TYR* 3.6 14.4 - - - -
315C SER 4.7 7.4 - - - +
316C TYR* 3.5 5.6 - - - -
317C ASN* 3.0 33.3 + - + +
320C VAL* 4.0 20.7 - - + +
504C ARG* 2.6 55.2 + - - +
507C ARG* 1.3 104.4 + - - +
509C GLY* 1.3 57.8 + - - +
510C ASP 3.4 0.4 - - - -
6E FUC 4.6 2.4 - - - +
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Residues in contact with GLY 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASN* 3.7 6.8 - - - +
16A ASN* 4.9 3.7 + - - +
170C PHE* 3.7 0.3 - - - -
316C TYR* 3.6 12.9 + - - -
317C ASN 4.0 3.8 - - - -
320C VAL* 3.7 22.7 - - - +
322C PRO* 3.6 25.0 - - - +
505C LYS 2.8 18.6 + - - -
507C ARG 3.2 0.2 - - - -
508C ASP* 1.3 77.5 - - - +
510C ASP* 1.3 58.1 + - - +
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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
------------------------------------------------------------
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