Contacts of the strand formed by residues 61 - 67 (chain A) in PDB entry 3PHM
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 4.2 0.2 - - - +
57A LEU* 2.9 29.0 + - + -
58A ASP* 3.0 29.1 + - + +
59A ALA 3.5 0.2 - - - -
60A SER* 1.3 83.9 + - - +
62A PHE* 1.3 65.6 + - - +
192A HIS* 2.8 31.7 + - + +
193A LEU 3.4 2.9 - - - -
194A THR* 2.8 22.4 + - - -
195A ARG* 4.6 0.4 - - - -
704A GOL 2.9 27.3 + - - -
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Residues in contact with PHE 62 (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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54A VAL* 4.2 14.4 - - + -
55A THR 3.4 14.6 - - - +
56A PRO* 4.2 6.5 - - + -
57A LEU* 3.7 7.6 - - - -
61A ASP* 1.3 76.3 - - - +
63A ALA* 1.3 69.6 + - - +
64A LEU* 4.3 9.4 - - + -
86A LEU* 6.4 0.4 - - + -
87A PRO* 3.5 33.2 - - + -
88A VAL* 4.2 20.2 - - + -
92A ALA* 5.4 2.7 - - + -
191A VAL 3.8 0.2 - - - +
192A HIS* 3.8 0.3 - - - -
193A LEU* 2.9 66.7 + - + +
194A THR 5.4 0.2 - - - -
195A ARG* 3.6 37.0 - - + +
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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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53A PRO 3.5 1.2 - - - +
54A VAL* 3.5 3.1 - - - -
55A THR* 2.9 42.0 + - - +
57A LEU* 3.5 23.6 - - + +
62A PHE* 1.3 76.5 - - - +
64A LEU* 1.3 59.4 + - - +
65A ASP* 5.1 3.4 - - - +
190A SER* 4.0 14.8 - - - +
191A VAL 3.2 10.5 - - - +
192A HIS* 4.9 1.1 - - + -
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Residues in contact with LEU 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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53A PRO* 3.3 9.9 - - + +
54A VAL* 3.9 19.1 - - + -
62A PHE* 4.0 6.9 + - + -
63A ALA* 1.3 73.2 - - - +
65A ASP* 1.3 59.8 + - - +
66A ILE* 3.8 11.1 + - + -
84A MET* 3.7 31.2 - - + -
85A ARG 4.8 2.0 - - - +
87A PRO* 3.9 25.4 - - + -
167A PHE* 3.8 35.4 - - + -
189A VAL 3.8 1.0 - - - +
190A SER* 3.5 0.7 - - - -
191A VAL* 2.7 39.2 + - + +
193A LEU* 4.2 14.6 - - + -
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Residues in contact with ASP 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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48A LEU* 3.4 29.2 - - + -
53A PRO* 2.8 32.7 + - - +
55A THR* 5.1 5.5 + - - -
63A ALA* 5.1 4.0 - - - +
64A LEU* 1.3 72.8 + - - +
66A ILE* 1.3 61.7 + - - +
67A ARG* 2.8 29.2 + - - +
84A MET* 3.5 9.2 - - - +
100A ARG* 2.8 23.8 + - - +
189A VAL 3.7 2.5 - - - -
190A SER* 3.3 20.9 + - - -
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Residues in contact with ILE 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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64A LEU* 4.1 10.3 - - + +
65A ASP* 1.3 75.2 - - - +
67A ARG* 1.3 59.0 + - - +
82A MET* 3.7 23.1 - - - -
84A MET* 3.7 21.1 - - + -
111A LEU* 3.8 12.3 - - + -
167A PHE* 3.6 35.9 - - + +
169A LEU* 3.5 21.3 - - + +
188A GLY* 3.0 4.5 - - - -
189A VAL* 2.8 40.9 + - + +
191A VAL* 3.5 27.8 - - + -
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Residues in contact with ARG 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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45A ASN* 2.6 56.8 + - - +
46A GLU 2.9 13.9 + - - -
47A CYS* 6.1 0.2 - - - -
48A LEU* 3.7 24.4 - - + +
65A ASP* 2.8 40.6 + - + +
66A ILE* 1.3 82.8 - - - +
68A MET* 1.3 71.9 + - - +
69A PRO* 3.4 1.4 - - - +
82A MET* 3.2 25.4 - - - +
84A MET* 5.8 0.4 - - - -
100A ARG* 3.4 17.7 - - - +
169A LEU* 4.4 0.4 - - - -
186A CYS* 2.9 23.0 + - + +
187A SER 3.5 3.6 - - - -
188A GLY* 4.1 9.9 - - - -
189A VAL 4.5 0.4 - - - +
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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