Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 3DLX
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 PRO 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.0 15.3 - - + -
62A GLY 3.4 19.5 - - - +
68A GLY 4.0 3.1 - - - +
69A ILE* 1.4 80.9 - - + +
71A GLU* 1.3 63.4 + - - +
73A LEU* 4.2 4.7 - - + -
74A ILE* 3.1 25.1 + - + +
209A LEU* 3.4 26.9 - - + +
210A VAL 4.0 4.0 - - - -
211A LYS* 3.7 18.4 - - + +
244A GLU* 3.0 28.4 - - + +
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Residues in contact with GLU 71 (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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69A ILE* 2.9 22.6 + - + +
70A PRO* 1.3 73.2 - - - +
72A ASN* 1.3 71.0 + - - +
74A ILE* 3.7 6.3 + - - +
75A ASP* 3.2 25.6 + - - +
97A PHE* 3.8 27.0 - - + -
98A GLY 6.2 0.4 - - - +
101A LEU* 5.8 1.4 - - - +
211A LYS* 5.6 0.2 - - - -
244A GLU* 3.5 2.0 + - - -
274A LYS 3.7 3.9 - - - +
275A TYR* 3.5 21.1 - - + -
276A GLU* 2.8 38.3 + - - +
277A LYS* 3.5 23.2 + - - +
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Residues in contact with ASN 72 (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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46A PRO* 4.3 11.3 - - + +
71A GLU* 1.3 76.0 - - - +
73A LEU* 1.3 61.9 + - - +
74A ILE 3.4 0.2 - - - -
75A ASP* 3.6 7.6 + - - +
76A ALA* 3.1 24.8 + - - +
244A GLU* 2.9 26.0 + - - +
270A ILE* 4.4 8.3 - - + -
272A GLY* 3.7 16.1 - - - -
273A GLU* 3.5 7.6 + - - +
274A LYS* 2.8 42.3 + - - +
275A TYR* 3.3 19.2 + - - -
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Residues in contact with LEU 73 (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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46A PRO* 4.7 7.4 - - + +
49A ALA* 5.0 1.1 - - + -
50A VAL* 3.8 15.0 - - + -
70A PRO* 3.8 6.5 - - + +
72A ASN* 1.3 75.8 - - - +
74A ILE* 1.3 61.2 + - - +
76A ALA* 3.3 4.4 + - - +
77A LEU* 2.9 31.8 + - - +
209A LEU* 4.1 19.5 - - + -
210A VAL 4.0 11.2 - - - +
242A VAL* 3.5 50.9 - - + +
244A GLU* 2.9 33.7 + - - +
270A ILE* 3.8 21.5 - - + -
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Residues in contact with ILE 74 (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 VAL* 4.3 23.1 - - + -
69A ILE* 3.7 21.1 - - + -
70A PRO* 3.1 22.8 + - + +
71A GLU* 4.0 6.5 - - - +
72A ASN 3.4 0.2 - - - -
73A LEU* 1.3 77.5 - - - +
75A ASP* 1.3 61.3 + - - +
77A LEU* 3.2 9.3 + - - +
78A LEU* 3.1 20.8 + - - +
98A GLY* 3.5 38.4 - - - +
99A LEU* 4.1 2.9 - - - +
101A LEU* 4.0 20.0 - - + -
102A LEU* 3.9 26.0 - - + +
209A LEU* 4.9 4.9 - - + -
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Residues in contact with ASP 75 (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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71A GLU 3.2 18.2 + - - +
72A ASN* 3.6 9.4 - - - +
73A LEU 3.3 0.2 - - - -
74A ILE* 1.3 78.7 - - - +
76A ALA* 1.3 59.4 + - - +
78A LEU* 3.3 22.5 + - + +
79A LYS* 3.1 51.3 + - - +
101A LEU* 5.6 2.6 - - + +
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Residues in contact with ALA 76 (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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46A PRO* 3.6 36.8 - - + +
47A VAL* 3.9 13.2 - - + +
50A VAL* 3.7 9.6 - - + -
72A ASN 3.1 14.2 + - - +
73A LEU* 3.5 11.0 - - - +
74A ILE 3.3 0.4 - - - -
75A ASP* 1.3 78.1 + - - +
77A LEU* 1.3 56.7 + - - +
79A LYS* 3.3 5.1 + - - +
80A THR* 3.1 31.5 + - - +
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Residues in contact with LEU 77 (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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50A VAL* 3.8 26.0 - - + -
53A ILE* 4.2 15.0 - - + -
59A VAL* 4.9 5.2 - - + -
61A VAL* 6.4 0.2 - - + -
73A LEU 2.9 25.9 + - - +
74A ILE* 3.2 7.3 + - - +
76A ALA* 1.3 71.8 - - - +
78A LEU* 1.3 60.5 + - - +
80A THR* 3.2 7.3 + - - +
81A GLY 2.9 16.6 + - - -
82A VAL* 4.1 9.6 - - + -
85A LEU* 4.3 18.2 - - + -
102A LEU* 4.0 25.1 - - + -
107A GLN* 2.8 23.4 + - - +
209A LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 78 (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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74A ILE 3.1 15.3 + - - +
75A ASP* 3.3 28.9 + - - +
77A LEU* 1.3 77.6 - - - +
79A LYS* 1.3 62.4 + - + +
81A GLY* 3.6 8.5 + - - -
101A LEU* 3.6 50.9 - - + +
102A LEU* 3.7 8.3 - - + -
105A SER* 3.6 20.0 - - - +
107A GLN* 3.7 8.4 - - - +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.0 25.1 - - + -
75A ASP* 3.1 37.2 + - - +
76A ALA* 3.5 7.2 - - - +
77A LEU 3.2 0.4 - - - -
78A LEU* 1.3 78.9 - - + +
80A THR* 1.3 59.9 + - - +
81A GLY* 4.8 0.2 - - - -
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Residues in contact with THR 80 (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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47A VAL* 3.7 25.8 - - + -
50A VAL* 4.3 16.1 + - + +
51A LYS* 4.5 15.0 - - + -
76A ALA 3.1 13.1 + - - +
77A LEU* 3.2 15.9 + - - +
78A LEU 3.4 0.2 - - - -
79A LYS* 1.3 76.5 - - - +
81A GLY* 1.3 65.0 + - - +
82A VAL* 3.2 17.2 + - - +
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Residues in contact with GLY 81 (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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55A ASP* 5.0 0.2 - - - +
77A LEU 2.9 12.9 + - - -
78A LEU 3.6 6.9 + - - -
79A LYS 3.4 2.6 - - - -
80A THR* 1.3 78.3 - - - +
82A VAL* 1.3 66.4 + - - +
83A LYS* 3.3 14.4 + - - +
107A GLN* 3.5 13.1 + - - +
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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
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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