Contacts of the strand formed by residues 100 - 107 (chain C) in PDB entry 5AQP
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 ARG 100 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG 4.8 2.8 + - - +
77C ARG* 4.0 15.9 - - - +
78C PHE* 4.0 3.1 - - - -
95C VAL 3.6 0.5 - - - +
96C ASN* 3.6 0.4 + - - -
97C ASP* 2.8 41.6 + - - +
98C ALA* 4.5 3.6 - - - +
99C GLY* 1.3 81.5 - - - +
101C PRO* 1.4 69.8 - - + +
115C TYR* 3.6 43.1 + - + -
116C PRO* 5.1 2.2 - - - +
117C GLU* 2.7 40.6 + - - -
157C ALA* 6.0 0.8 - - - +
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Residues in contact with PRO 101 (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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73C LEU* 4.0 28.9 - - + +
76C ARG 3.0 29.8 - - - +
77C ARG 4.5 1.6 - - - +
78C PHE* 3.6 19.9 - - + +
83C VAL* 4.4 3.8 - - + -
94C VAL* 3.8 20.4 - - + -
95C VAL 3.3 7.2 - - - +
100C ARG* 1.4 83.5 - - + +
102C LYS* 1.3 67.5 + - - +
115C TYR* 3.9 4.0 - - - -
116C PRO* 3.4 23.9 - - + +
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Residues in contact with LYS 102 (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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73C LEU* 5.9 0.4 - - - -
94C VAL* 3.3 4.5 - - - -
95C VAL* 2.8 45.8 + - + +
97C ASP* 3.4 35.8 + - + +
101C PRO* 1.3 80.3 - - - +
103C VAL* 1.3 61.0 - - - +
113C SER* 2.9 38.8 + - - +
114C PHE 3.3 25.4 - - - +
115C TYR* 3.7 37.0 + - + +
116C PRO* 4.8 0.9 - - - -
118C GLU* 4.8 1.4 + - - -
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Residues in contact with VAL 103 (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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44C PHE* 5.7 0.4 - - + -
67C VAL* 3.9 29.2 - - + -
70C ALA* 6.1 1.3 - - + -
73C LEU* 3.8 21.7 - - + +
92C PHE* 3.8 27.4 - - + -
93C MET 3.3 7.0 - - - +
94C VAL* 4.2 2.0 - - + +
102C LYS* 1.3 72.2 - - - +
104C GLN* 1.3 60.1 + - - +
105C VAL* 5.0 2.0 - - + -
112C LYS 4.0 0.3 - - - +
113C SER* 3.2 3.9 - - - -
114C PHE* 2.9 51.2 + - + +
116C PRO* 5.5 3.6 - - + +
119C VAL* 3.8 23.3 - - + -
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Residues in contact with GLN 104 (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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358A GLU* 3.4 42.2 - - - +
64C THR 4.7 1.9 - - - +
92C PHE* 4.9 0.2 - - - +
93C MET* 2.8 57.2 + - + +
95C VAL* 3.6 33.5 - - + +
102C LYS 3.7 0.2 + - - -
103C VAL* 1.3 73.2 - - - +
105C VAL* 1.3 70.4 + - - +
111C THR* 3.8 23.1 - - + +
112C LYS 3.5 7.9 - - - +
113C SER* 4.3 5.8 - - - +
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Residues in contact with VAL 105 (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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44C PHE* 3.5 31.9 - - + -
64C THR 4.2 2.9 - - - +
65C ASN* 3.8 25.4 - - - +
67C VAL* 3.8 29.4 - - + -
92C PHE* 5.0 1.1 - - + -
103C VAL* 5.0 2.2 - - + -
104C GLN* 1.3 82.3 - - - +
106C GLU* 1.3 64.4 + - - +
107C TYR* 4.4 3.1 - - + -
111C THR* 3.4 6.9 - - - +
112C LYS 2.8 40.0 + - - +
114C PHE* 4.0 14.8 - - + -
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Residues in contact with GLU 106 (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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44C PHE* 3.7 14.4 - - - +
45C THR 4.5 2.5 - - - +
65C ASN* 2.9 37.0 + - - +
105C VAL* 1.3 72.9 - - - +
107C TYR* 1.3 59.1 + - - +
108C LYS 4.3 0.4 - - - -
109C GLY* 4.3 24.2 + - - +
110C GLU 3.4 11.9 - - - +
111C THR* 4.6 7.7 + - - +
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Residues in contact with TYR 107 (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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44C PHE* 3.6 38.4 - + + -
45C THR 3.7 7.9 - - - -
48C GLU* 3.7 23.1 - - - -
49C ARG* 3.7 26.4 + - + +
105C VAL* 3.9 1.8 + - + -
106C GLU* 1.3 71.7 - - - +
108C LYS* 1.4 108.1 + - + +
109C GLY 3.3 0.4 - - - -
110C GLU* 2.8 27.7 + - - +
112C LYS* 4.1 29.6 - - + +
114C PHE* 4.4 7.6 - + - -
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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