Contacts of the helix formed by residues 60 - 69 (chain A) in PDB entry 1D2V
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 4.1 9.9 - - - +
59A ALA* 1.3 71.2 - - - +
61A ALA* 1.3 66.0 + - - +
63A ALA* 2.9 29.7 + - + +
64A VAL* 3.0 12.3 + - - +
129C LYS* 3.7 48.9 - - + +
130C ILE 3.6 9.9 - - - +
131C PRO* 3.4 37.2 - - + -
132C PRO* 5.3 1.8 - - + -
426C ARG* 4.3 2.0 - - - +
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Residues in contact with ALA 61 (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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59A ALA 3.2 5.8 + - - -
60A LEU* 1.3 70.6 - - - +
62A ARG* 1.3 57.4 + - - +
64A VAL* 3.3 6.6 + - - +
65A SER* 2.9 27.9 + - - -
128C LEU* 4.1 9.5 - - + +
419C ALA* 3.2 32.3 - - + +
422C MET* 3.7 18.9 - - + +
423C GLN* 4.0 11.4 + - - +
426C ARG* 3.6 14.4 - - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.1 1.0 - - - +
61A ALA* 1.3 75.9 - - - +
63A ALA* 1.3 61.0 + - - +
65A SER* 4.2 0.4 - - - -
66A ASN* 2.9 45.2 + - - -
128C LEU* 4.6 4.6 - - + +
129C LYS 3.9 17.4 + - - +
130C ILE* 4.4 5.2 - - + -
131C PRO* 3.5 10.3 - - + -
134C ASP* 2.8 40.5 + - - +
135C PRO* 4.5 1.2 - - - +
136C ARG* 3.7 19.8 - - - +
137C ILE* 4.6 3.0 - - - +
144C ILE* 3.8 24.3 - - + +
403C ARG* 3.2 15.4 + - - +
404C GLU* 2.7 36.8 + - - -
416C ASP* 2.8 34.1 + - - -
419C ALA* 3.8 6.8 - - + +
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Residues in contact with ALA 63 (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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60A LEU* 2.9 24.1 + - + +
62A ARG* 1.3 80.6 - - - +
64A VAL* 1.4 56.4 + - - +
66A ASN* 3.1 3.5 + - - +
67A GLU* 2.9 34.2 + - + +
131C PRO* 3.8 27.5 - - + +
467C GLN* 3.2 19.7 - - - +
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Residues in contact with VAL 64 (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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59A ALA* 3.9 16.4 - - + +
60A LEU 3.0 18.1 + - - +
61A ALA* 3.6 7.9 - - - +
63A ALA* 1.4 74.4 - - - +
65A SER* 1.3 58.5 + - - +
68A ILE* 2.9 37.1 + - + +
69A VAL* 3.5 0.7 + - - +
422C MET* 3.4 16.8 - - - -
426C ARG* 4.7 0.4 - - - +
467C GLN* 3.4 18.4 - - + +
468C TYR* 3.4 41.7 - - + +
478C MET* 3.6 19.1 - - + -
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Residues in contact with SER 65 (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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61A ALA 2.9 17.3 + - - -
62A ARG 3.7 3.6 - - - -
64A VAL* 1.3 77.5 - - - +
66A ASN* 1.3 56.6 + - - +
69A VAL* 3.0 16.6 + - - +
70A ARG 3.0 26.2 + - - -
403C ARG* 2.9 17.1 + - - +
416C ASP* 2.8 37.7 + - - -
418C PRO* 3.9 3.1 - - - +
419C ALA* 3.9 8.7 - - - -
422C MET* 3.9 2.9 - - - +
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Residues in contact with ASN 66 (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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62A ARG* 2.9 36.3 + - - +
63A ALA* 3.1 4.9 + - - +
65A SER* 1.3 77.7 - - - +
67A GLU* 1.3 72.8 + - - +
70A ARG* 3.2 29.4 + - - +
131C PRO* 3.6 14.1 - - - +
134C ASP* 3.0 28.5 + - - -
135C PRO* 3.8 18.3 - - + +
403C ARG* 2.8 34.4 + - - +
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Residues in contact with GLU 67 (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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63A ALA* 2.9 20.6 + - + +
66A ASN* 1.3 88.0 + - - +
68A ILE* 1.3 62.8 + - + +
70A ARG 5.2 1.5 - - - +
463C LYS* 4.1 23.0 + - + +
467C GLN* 3.7 31.6 - - + +
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Residues in contact with ILE 68 (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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64A VAL* 2.9 22.1 + - + +
67A GLU* 1.3 86.1 - - + +
69A VAL* 1.3 61.5 + - - +
70A ARG 3.7 4.3 - - - +
394C GLN 4.7 4.0 - - - +
395C ASN* 5.7 2.9 - - - -
397C ILE* 3.8 11.3 - - + +
460C LEU* 4.0 22.4 - - + -
463C LYS* 3.8 19.9 - - + +
464C LEU* 3.4 43.7 - - + +
467C GLN* 4.0 17.7 - - + -
478C MET* 3.8 26.7 - - + -
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Residues in contact with VAL 69 (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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64A VAL 4.3 0.2 - - - +
65A SER* 3.0 24.6 + - - +
68A ILE* 1.3 75.5 - - - +
70A ARG* 1.3 69.8 + - - +
71A PHE* 3.4 9.4 + - - +
395C ASN 5.7 0.5 - - - -
397C ILE* 4.1 12.4 + - + -
398C ALA* 3.6 46.1 + - + +
403C ARG* 3.9 3.8 - - - -
418C PRO* 3.8 15.9 - - + -
422C MET* 4.5 0.7 - - + -
477C TRP* 4.0 11.4 - - + -
478C MET* 3.8 34.5 - - + -
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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