Contacts of the helix formed by residues 68 - 73 (chain A) in PDB entry 2WWA
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 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.6 34.0 + - + +
67A PHE* 1.4 100.1 - - + +
69A ARG* 1.4 62.7 + - - +
70A GLY 3.3 0.5 + - - -
71A VAL* 3.4 5.4 + - - +
72A PHE* 3.0 64.1 + - + -
74A CYS* 5.1 2.5 - - - -
135A PHE* 4.1 13.5 - - + -
304A PHE* 4.0 14.8 - - + -
311A PHE* 4.6 0.4 - - + -
312A VAL* 3.5 32.8 - - + -
315A GLN* 5.9 1.3 - - - +
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Residues in contact with ARG 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 PRO* 5.2 0.2 - - - +
65A ILE 4.0 12.7 + - - +
66A TYR* 3.6 36.9 + - - -
67A PHE 3.4 3.2 - - - +
68A LEU* 1.4 78.4 - - - +
70A GLY* 1.4 61.5 + - - +
71A VAL 3.5 0.5 + - - -
73A GLY 3.6 14.9 + - - -
74A CYS* 3.7 30.3 + - - +
75A GLU* 3.3 34.3 + - - +
76A PRO* 4.0 22.6 - - + +
77A ARG* 5.1 6.3 - - - +
188A VAL* 3.9 6.4 - - - +
191A THR* 4.4 4.6 + - - +
192A ASN* 3.0 42.5 + - - +
195A ALA* 5.6 4.9 - - - +
448A GLY* 4.4 12.6 - - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE 4.4 4.5 + - - -
68A LEU 3.3 1.2 + - - -
69A ARG* 1.4 78.1 - - - +
71A VAL* 1.4 57.0 + - - +
73A GLY 4.6 0.8 + - - -
185A ASN* 4.2 6.8 + - - +
188A VAL* 4.0 11.5 - - - +
300A TYR* 5.2 4.9 - - - -
448A GLY* 4.6 0.8 - - - -
449A LYS* 3.8 30.2 - - - +
450A ALA 4.9 1.1 - - - -
451A ALA 5.4 0.9 - - - -
452A GLY* 3.7 22.8 - - - -
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Residues in contact with VAL 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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67A PHE 4.6 0.6 + - - +
68A LEU 3.6 10.3 - - - +
70A GLY* 1.4 74.1 - - - +
72A PHE* 1.4 75.7 + - + +
73A GLY 3.4 1.3 - - - -
84A LEU* 5.0 6.4 - - - +
85A PHE* 4.6 7.0 + - + -
88A ILE* 5.6 4.1 - - + +
185A ASN* 4.0 12.0 - - - +
297A LEU* 4.7 16.7 - - + +
300A TYR* 3.6 29.7 - - + -
301A THR* 3.7 25.4 - - - +
304A PHE* 3.8 31.6 - - + -
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Residues in contact with PHE 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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68A LEU* 3.0 68.3 + - + +
69A ARG 4.3 0.2 - - - +
71A VAL* 1.4 82.5 - - + +
73A GLY* 1.4 57.2 + - - +
74A CYS* 3.5 18.6 - - + -
81A GLU 3.4 21.8 - - - -
82A PHE* 3.3 32.3 - + - +
84A LEU* 2.9 34.7 + - - +
85A PHE* 3.3 60.3 - + + +
131A LEU* 6.0 0.4 - - + -
135A PHE* 5.1 4.5 - + - -
312A VAL* 4.7 2.0 - - + -
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Residues in contact with GLY 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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43A TYR* 3.5 20.4 - - - -
69A ARG 3.6 4.6 + - - -
70A GLY 4.6 1.0 - - - -
71A VAL 3.4 2.8 - - - +
72A PHE* 1.4 78.7 - - - +
74A CYS* 1.4 58.6 + - - +
80A LEU* 4.7 0.5 - - - +
83A GLY* 4.2 5.8 - - - -
84A LEU* 5.5 0.4 - - - -
184A ILE* 4.0 24.6 - - - +
185A ASN* 5.0 5.4 + - - -
188A VAL* 3.6 26.2 - - - -
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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