Contacts of the helix formed by residues 495 - 508 (chain I) in PDB entry 6C6U
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 ALA 495 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123I TYR* 4.0 20.1 + - + +
124I MET* 3.8 14.1 - - - +
125I GLY* 3.5 23.8 - - - +
494I ASN* 1.3 72.4 - - - +
496I LYS* 1.3 66.8 + - + +
497I PRO 3.7 0.4 - - - -
498I ILE* 4.4 5.2 - - - -
499I SER* 3.3 25.2 + - - -
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Residues in contact with LYS 496 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B G 3.4 34.8 - - - +
494I ASN* 3.2 12.7 - - + +
495I ALA* 1.3 82.0 - - + +
497I PRO* 1.3 68.1 - - + +
499I SER* 4.3 1.0 - - - -
500I ALA* 2.9 31.5 + - - +
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Residues in contact with PRO 497 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B G 4.7 7.9 - - - +
467I GLY* 4.3 7.6 - - - +
470I ARG* 4.4 35.0 + - + +
471I VAL* 5.0 8.3 - - + +
474I ALA* 6.2 2.0 - - + -
494I ASN* 3.7 24.7 - - - +
496I LYS* 1.3 92.1 - - + +
498I ILE* 1.3 60.1 + - + +
500I ALA* 3.8 5.6 - - + +
501I ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 498 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I LEU* 5.5 0.2 - - + -
124I MET* 4.8 15.5 - - + -
125I GLY* 4.2 19.5 - - - +
127I ILE* 6.1 0.4 - - + -
464I PHE* 3.5 32.9 - - + +
467I GLY* 4.1 20.6 - - - +
468I LEU* 4.6 13.5 - - + +
471I VAL* 3.7 33.4 - - + -
493I ILE* 5.0 4.0 - - + -
494I ASN 3.8 18.2 - - - +
495I ALA* 4.6 5.2 - - - +
496I LYS 3.4 0.4 - - - -
497I PRO* 1.3 76.4 - - + +
499I SER* 1.3 59.6 + - - +
501I ALA* 3.3 2.4 + - - +
502I VAL* 3.0 31.3 + - + +
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Residues in contact with SER 499 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLY* 3.8 17.5 - - - -
126I GLU* 4.4 9.8 + - - +
495I ALA* 3.3 19.6 + - - -
496I LYS* 4.3 0.9 - - - -
498I ILE* 1.3 80.3 - - - +
500I ALA* 1.3 57.5 + - - +
502I VAL* 3.7 8.8 - - - +
503I LYS* 2.8 46.4 + - - +
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Residues in contact with ALA 500 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B A 6.2 4.9 - - - -
26B G 6.1 0.2 - - - +
470I ARG* 5.9 3.4 - - - +
496I LYS 2.9 22.9 + - - +
497I PRO* 3.8 6.1 - - + +
499I SER* 1.3 76.9 - - - +
501I ALA* 1.3 56.3 + - - +
503I LYS* 3.8 4.2 - - - +
504I GLU* 2.9 36.1 + - - +
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Residues in contact with ALA 501 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I GLN* 3.8 30.2 + - + +
464I PHE* 5.6 0.4 - - - -
466I VAL* 5.6 3.1 - - + -
467I GLY* 4.1 13.0 - - - +
470I ARG* 4.9 12.7 - - - +
497I PRO 2.9 18.1 + - - +
498I ILE 3.7 3.4 - - - +
500I ALA* 1.3 76.6 - - - +
502I VAL* 1.3 57.3 + - - +
504I GLU* 3.3 7.9 + - - +
505I PHE* 3.0 28.1 + - - +
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Residues in contact with VAL 502 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 6.4 0.9 - - + -
126I GLU 4.0 20.9 - - - +
127I ILE* 4.4 21.1 - - + -
128I PRO* 4.6 2.2 - - + -
460I ALA* 5.2 12.1 - - + +
463I GLN* 5.0 5.4 + - + -
464I PHE* 5.1 12.6 - - + -
498I ILE* 3.0 24.5 + - + +
499I SER* 3.7 10.3 - - - +
501I ALA* 1.3 77.6 - - - +
503I LYS* 1.3 62.0 + - + +
505I PHE* 3.4 6.7 + - + +
506I PHE* 3.0 54.8 + - + +
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Residues in contact with LYS 503 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I THR* 4.8 19.6 - - + +
126I GLU 6.0 0.7 - - - +
128I PRO* 6.2 2.2 - - - -
138I ILE* 5.6 4.3 - - + +
139I ASN* 5.6 6.7 - - - +
499I SER* 2.8 31.1 + - - +
500I ALA* 4.1 4.3 - - - +
502I VAL* 1.3 76.6 - - + +
504I GLU* 1.3 60.9 + - - +
506I PHE* 4.6 2.6 - - - +
507I GLY* 2.9 27.4 + - - +
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Residues in contact with GLU 504 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463I GLN* 6.3 0.2 - - - +
470I ARG* 5.5 4.3 + - - -
500I ALA* 2.9 21.8 + - - +
501I ALA* 3.8 6.2 - - - +
503I LYS* 1.3 76.7 - - - +
505I PHE* 1.3 60.1 + - - +
508I SER* 3.0 45.0 + - - +
320J ASN* 4.0 21.7 + - - +
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Residues in contact with PHE 505 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ILE* 4.5 12.6 - - + -
456I VAL 5.1 0.7 - - - -
459I MET* 3.7 38.4 - - + -
460I ALA* 4.2 16.6 - - - -
463I GLN* 3.6 40.3 - - + +
501I ALA 3.0 16.9 + - - +
502I VAL* 3.8 4.9 - - + +
504I GLU* 1.3 77.6 - - - +
506I PHE* 1.3 94.0 + + - +
507I GLY 3.4 0.3 + - - -
509I SER* 3.4 44.8 + - - -
511I LEU* 5.5 4.0 - - + -
512I SER* 3.5 6.7 - - - -
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Residues in contact with PHE 506 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I PHE* 4.9 4.5 - + - -
38I PHE* 6.0 1.1 - + - -
127I ILE* 5.4 2.2 - - + -
128I PRO* 3.5 46.9 - - + -
136I PHE* 4.3 14.1 - + - -
138I ILE* 3.7 28.5 - - + +
143I ARG* 3.5 7.6 + - - -
145I ILE* 3.6 25.8 - - + -
456I VAL* 4.6 7.4 - - + -
460I ALA* 3.8 22.7 - - + -
502I VAL* 3.0 29.2 + - + +
503I LYS* 4.6 2.2 - - - +
505I PHE* 1.3 103.0 - + - +
507I GLY* 1.3 58.3 + - - +
512I SER* 2.9 17.9 + - - -
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Residues in contact with GLY 507 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B C 4.4 8.3 - - - +
138I ILE* 4.2 11.0 - - - -
143I ARG* 2.3 35.0 + - - -
503I LYS 2.9 20.3 + - - -
504I GLU* 4.9 0.2 - - - -
506I PHE* 1.3 78.7 - - - +
508I SER* 1.3 66.6 + - - +
509I SER 4.1 0.9 - - - -
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Residues in contact with SER 508 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B T 5.1 3.5 + - - -
22B C 3.3 28.7 + - - -
143I ARG* 4.7 2.9 + - - +
503I LYS 4.5 0.2 + - - -
504I GLU* 3.0 27.1 + - - +
507I GLY* 1.3 78.9 + - - +
509I SER* 1.3 61.0 + - - +
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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