Contacts of the strand formed by residues 46 - 51 (chain C) in PDB entry 3AP4
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 PHE 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 4.2 3.4 - - + -
45C ARG* 1.3 75.5 - - - +
47C GLN* 1.3 71.3 + - - +
48C VAL* 3.9 22.4 - - + -
67C ASN* 2.6 27.1 + - - -
68C PRO* 3.0 47.0 + - + +
70C PHE* 4.0 21.8 - + - -
97C PHE* 4.2 10.1 - + - -
103C PHE* 3.9 26.2 - + - -
105C ILE* 4.2 5.8 - - + -
140C ILE* 4.7 1.6 - - + -
141C TYR 3.3 15.0 - - - +
142C GLY* 4.3 1.3 - - - -
143C LYS 3.8 7.6 - - - +
144C VAL* 3.5 42.4 - - + -
146C ILE* 5.5 0.9 - - + -
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG* 2.8 29.7 + - - +
46C PHE* 1.3 76.7 - - - +
48C VAL* 1.3 62.9 + - - +
49C ASP* 2.7 29.0 + - - +
59C ARG* 3.9 14.1 - - - +
65C HIS* 3.3 30.4 + - + +
66C PHE 3.1 9.4 - - - +
67C ASN* 4.0 1.8 - - - +
140C ILE* 3.3 9.7 - - - +
141C TYR* 3.0 57.2 + - + +
142C GLY* 5.8 0.5 - - - -
2G GAL 5.2 1.6 + - - -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.7 26.9 - - + -
46C PHE* 3.9 20.6 - - + -
47C GLN* 1.3 77.2 - - - +
49C ASP* 1.3 61.2 + - - +
50C LEU* 4.5 4.0 - - + +
64C PHE* 3.5 3.8 - - - +
66C PHE* 2.8 50.5 + - + +
105C ILE* 4.5 6.1 - - + -
107C ILE* 4.1 16.2 - - + -
138C LEU* 3.6 26.2 - - + -
139C GLY 3.6 3.4 - - - -
140C ILE* 4.5 9.9 - - + -
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLN* 2.7 30.4 + - - +
48C VAL* 1.3 80.8 - - - +
50C LEU* 1.3 66.0 + - - +
51C GLN* 3.7 17.8 + - + +
59C ARG* 4.1 7.4 + - - -
62C VAL* 3.9 16.0 - - + +
64C PHE 3.4 2.5 - - - -
65C HIS* 2.7 30.9 + - - -
137C THR 3.6 0.3 - - - +
138C LEU* 3.5 5.9 - - - +
139C GLY 2.7 41.0 + - - +
141C TYR* 3.3 12.5 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 4.9 5.8 - - + -
27C LEU* 4.1 16.2 - - + -
33C ILE* 3.9 20.4 - - + -
48C VAL* 4.5 8.7 - - + -
49C ASP* 1.3 77.2 - - - +
51C GLN* 1.3 59.7 + - - +
62C VAL* 3.6 1.0 - - - -
63C ALA* 2.8 29.3 + - - +
64C PHE* 2.9 31.7 + - + +
107C ILE* 4.7 5.8 - - + -
114C PHE* 3.6 35.7 - - + -
135C ILE* 3.6 18.2 - - + -
137C THR 3.5 3.6 - - - +
138C LEU* 3.8 20.0 - - + -
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Residues in contact with GLN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 5.4 0.5 - - - +
49C ASP* 3.7 17.9 + - + +
50C LEU* 1.3 77.1 - - - +
52C ASN* 1.3 59.9 + - - +
53C GLY 3.1 21.8 + - - +
54C SER* 4.0 9.9 - - - -
60C ALA* 4.1 7.6 - - + +
61C ASP 3.3 12.8 - - - +
62C VAL* 4.3 10.4 - - + +
135C ILE* 3.4 5.9 - - - -
136C ASP 3.0 23.9 + - - -
137C THR* 2.7 31.4 + - - +
139C GLY* 3.7 8.6 - - - -
141C TYR* 2.7 42.7 + - - -
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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