Contacts of the helix formed by residues 60 - 69 (chain B) in PDB entry 4EJX
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 LEU 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL 4.6 7.0 - - - +
59B ALA* 1.3 71.8 - - - +
61B ALA* 1.3 66.1 + - - +
62B ARG 4.3 1.8 - - - +
63B ALA* 3.2 17.7 + - + +
64B VAL* 3.1 21.5 + - - +
129D LYS* 3.4 55.4 - - + +
130D ILE 3.9 14.8 - - - +
131D PRO* 3.9 8.7 - - + -
426D ARG* 4.4 1.3 - - - +
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Residues in contact with ALA 61 (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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59B ALA 3.4 4.9 + - - -
60B LEU* 1.3 70.6 - - - +
62B ARG* 1.3 62.5 + - - +
64B VAL* 3.2 6.9 + - - +
65B SER* 3.0 23.2 + - - -
128D LEU* 3.8 12.5 - - + +
419D ALA* 3.3 30.1 - - - +
422D MET* 4.0 16.7 - - + +
423D GLN* 4.1 16.0 + - - +
426D ARG* 3.9 12.0 - - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.2 1.0 - - - +
61B ALA* 1.3 79.1 - - - +
63B ALA* 1.3 56.0 + - - +
65B SER* 3.5 1.2 - - - -
66B ASN* 3.0 48.3 + - - +
128D LEU* 4.3 5.3 - - + +
129D LYS 3.5 20.8 + - - +
130D ILE* 4.2 2.7 - - + -
131D PRO* 3.5 19.7 - - + -
134D ASP* 2.8 33.4 + - - +
135D PRO* 4.2 1.0 - - - +
136D ARG* 3.4 29.0 - - - +
137D ILE* 4.3 4.1 - - - +
144D ILE* 3.6 26.2 - - + +
403D ARG* 3.4 7.9 + - - +
404D GLU* 2.8 28.3 + - - -
416D ASP* 3.0 26.3 + - - +
419D ALA* 3.9 7.5 - - + +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 6.0 0.2 - - + -
60B LEU* 3.2 21.5 + - + +
62B ARG* 1.3 77.5 - - - +
64B VAL* 1.3 63.0 + - - +
66B ASN* 3.8 3.0 - - - +
67B GLU* 3.1 34.7 + - + +
131D PRO* 3.7 29.4 - - + +
467D GLN* 4.0 11.3 - - - +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 3.7 24.5 - - + +
60B LEU 3.1 17.0 + - - +
61B ALA* 3.2 6.5 + - - +
63B ALA* 1.3 72.4 - - - +
65B SER* 1.3 61.6 + - - +
68B ILE* 2.9 52.4 + - + +
69B VAL* 4.5 0.2 - - - +
422D MET* 3.7 16.6 - - + -
426D ARG* 4.7 0.9 - - - +
467D GLN* 3.8 13.9 - - + +
468D TYR* 3.4 33.4 - - + +
478D MET* 4.0 6.5 - - - -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.0 12.3 + - - -
62B ARG 3.5 7.2 - - - -
64B VAL* 1.3 76.6 - - - +
66B ASN* 1.3 56.7 + - - +
69B VAL* 2.9 33.6 + - - +
70B ARG 2.9 12.5 + - - -
403D ARG* 3.0 19.0 + - - +
416D ASP* 2.6 40.9 + - - -
418D PRO* 3.9 4.3 - - - +
419D ALA* 3.9 8.5 - - - -
422D MET* 4.0 3.2 - - - +
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Residues in contact with ASN 66 (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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62B ARG* 3.0 28.1 + - - +
63B ALA* 3.8 4.3 - - - +
64B VAL 3.4 0.2 - - - -
65B SER* 1.3 74.1 - - - +
67B GLU* 1.3 75.6 + - - +
70B ARG* 3.3 25.0 - - - +
131D PRO* 3.3 21.4 - - - +
134D ASP* 2.9 30.1 + - - +
135D PRO* 3.7 17.7 - - + +
403D ARG* 2.8 35.3 + - - +
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Residues in contact with GLU 67 (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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63B ALA* 3.1 21.6 + - + +
64B VAL 4.5 0.2 - - - +
66B ASN* 1.3 92.7 + - - +
68B ILE* 1.3 65.2 + - + +
70B ARG 5.5 1.7 - - - +
133D ASN 5.7 1.0 - - - +
463D LYS* 4.2 22.7 + - + +
466D GLU* 5.0 4.1 - - - +
467D GLN* 3.6 26.5 - - - +
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Residues in contact with ILE 68 (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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64B VAL* 2.9 25.4 + - + +
67B GLU* 1.3 84.4 - - + +
69B VAL* 1.3 62.5 + - - +
70B ARG 3.7 3.9 - - - +
394D GLN 4.8 2.6 - - - +
395D ASN* 5.7 3.1 - - - -
397D ILE* 3.6 13.2 + - + +
460D LEU* 3.9 22.9 - - + -
463D LYS* 4.0 21.8 - - + +
464D LEU* 3.7 27.6 - - + -
467D GLN* 3.8 28.5 - - + -
478D MET* 3.8 27.1 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL 4.5 0.2 - - - +
65B SER* 2.9 22.1 + - - +
68B ILE* 1.3 77.4 - - - +
70B ARG* 1.3 68.6 + - - +
71B PHE* 3.2 16.8 + - - +
395D ASN 5.4 0.5 - - - +
397D ILE* 4.3 11.9 + - + -
398D ALA* 3.7 25.6 + - + +
403D ARG* 3.8 10.5 - - - -
418D PRO* 3.5 40.8 - - + -
422D MET* 4.4 0.9 - - + -
477D TRP* 4.2 5.4 - - + -
478D MET* 3.9 25.6 - - + -
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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