Contacts of the strand formed by residues 73 - 85 (chain C) in PDB entry 2PQA
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 GLN 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLN* 4.0 21.6 + - - +
45C HIS 4.0 14.0 + - - +
46C ILE* 3.5 28.9 - - + +
47C VAL* 3.1 23.5 + - - +
72C SER* 1.3 81.7 + - - +
74C VAL* 1.3 66.7 + - - +
130C GLY 3.6 5.4 - - - +
131C HIS* 3.2 34.8 + - + +
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Residues in contact with VAL 74 (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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46C ILE* 3.8 7.7 - - - +
47C VAL 3.2 14.1 - - - +
49C CYS* 3.6 23.8 - - + -
54C LEU* 3.6 25.8 - - + -
71C ILE* 3.1 31.6 - - + -
72C SER 3.1 12.3 - - - +
73C GLN* 1.3 83.3 - - - +
75C THR* 1.3 66.6 + - - +
76C ILE* 4.6 0.4 - - + -
128C VAL 4.0 0.3 - - - +
129C ALA* 3.5 4.0 - - - +
130C GLY 3.1 33.8 + - - +
132C LEU* 4.9 2.2 - - + -
141C LEU* 5.1 8.7 - - + +
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Residues in contact with THR 75 (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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46C ILE* 3.9 13.4 - - + +
47C VAL 3.0 8.5 + - - -
48C PRO* 3.3 30.7 - - + -
49C CYS* 2.9 27.9 + - - +
74C VAL* 1.3 74.7 - - - +
76C ILE* 1.3 66.2 + - - +
127C LYS* 3.3 30.9 - - - +
128C VAL 3.1 15.9 + - - -
129C ALA* 4.7 4.9 - - - +
141C LEU* 5.9 0.4 - - - -
158C HIS* 3.3 13.6 + - + +
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Residues in contact with ILE 76 (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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49C CYS* 3.6 15.3 - - + +
51C ILE* 4.1 26.9 - - + +
54C LEU* 3.8 27.4 - - + -
74C VAL* 4.6 0.4 - - + -
75C THR* 1.3 78.4 + - - +
77C VAL* 1.3 65.3 + - - +
78C GLY 4.4 0.2 + - - -
94C ILE* 3.8 31.4 - - + -
96C ASP* 5.2 2.0 - - - +
102C MET* 5.7 0.4 - - - -
104C VAL* 4.5 6.3 - - + -
126C VAL 3.8 0.7 - - - +
127C LYS* 3.5 3.3 - - - +
128C VAL* 2.9 44.7 + - + -
141C LEU* 3.8 24.2 - - + +
158C HIS* 3.7 6.5 - - - -
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Residues in contact with VAL 77 (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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49C CYS 4.9 0.4 + - - -
51C ILE* 6.2 0.2 - - - -
76C ILE* 1.3 80.7 - - - +
78C GLY* 1.3 60.4 + - - +
96C ASP* 3.4 21.7 + - - +
125C TYR* 4.1 7.0 - - + -
126C VAL 3.3 8.7 - - - +
127C LYS* 3.9 25.1 - - + -
149C LEU* 3.9 23.3 - - + -
154C GLU 4.8 4.3 - - - +
155C PHE* 3.9 25.8 - - + -
158C HIS* 3.6 39.0 + - + +
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Residues in contact with GLY 78 (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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76C ILE 4.2 0.2 - - - -
77C VAL* 1.3 77.7 - - - +
79C ILE* 1.3 60.2 + - - -
94C ILE* 3.9 14.5 - - - +
95C ASP 3.4 17.3 - - - -
96C ASP* 4.0 1.3 - - - -
125C TYR* 3.5 12.8 - - - -
126C VAL* 2.9 35.5 + - - +
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Residues in contact with ILE 79 (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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78C GLY* 1.3 74.1 - - - -
80C ILE* 1.3 75.7 + - - +
81C ARG* 3.2 32.6 + - - +
94C ILE* 4.5 0.9 - - - -
95C ASP* 2.8 40.3 + - - +
97C MET* 3.9 7.4 - - + -
123C GLU* 3.3 43.1 - - - +
124C THR 3.3 11.0 - - - +
125C TYR* 4.0 26.2 - - + +
68D GLU* 5.4 0.7 - - - +
85D VAL* 3.8 17.5 - - + -
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Residues in contact with ILE 80 (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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79C ILE* 1.3 74.0 - - - +
81C ARG* 1.3 55.9 + - - +
82C HIS 3.8 15.0 - - - +
83C ALA* 4.7 0.4 - - + +
92C TYR* 3.7 37.5 - - + -
93C LYS 3.7 4.9 - - - +
94C ILE* 4.4 8.3 - - + +
120C VAL* 3.7 37.9 - - + +
121C PRO 3.9 14.6 - - - +
122C PRO* 2.6 41.0 - - + +
123C GLU 3.6 0.3 + - - -
124C THR 2.9 20.2 + - - +
126C VAL* 3.9 23.8 - - + -
146C ILE* 5.1 1.1 - - + -
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Residues in contact with ARG 81 (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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79C ILE* 3.6 17.9 - - - +
80C ILE* 1.3 77.0 - - - +
82C HIS* 1.3 60.3 + - + +
93C LYS* 2.7 18.6 + - + +
95C ASP* 2.8 44.8 + - + +
97C MET* 3.5 22.8 - - - +
101C PRO* 4.3 12.3 - - + -
122C PRO* 3.9 16.3 - - - +
123C GLU* 3.8 28.5 + - - +
5D MET* 3.3 32.1 - - - +
9D ARG* 4.3 1.6 - - - +
70D VAL* 4.9 3.6 - - - +
83D SER* 4.9 7.7 + - - -
85D VAL* 4.9 5.5 - - - +
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Residues in contact with HIS 82 (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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80C ILE* 3.6 8.5 - - - +
81C ARG* 1.3 82.7 - - + +
83C ALA* 1.3 86.4 + - - +
84C GLU* 3.7 23.8 + - + +
91C VAL 4.9 1.0 + - - -
92C TYR* 3.3 4.5 - - - -
93C LYS* 2.8 58.6 + - + +
122C PRO* 4.9 3.8 - - - -
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Residues in contact with ALA 83 (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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80C ILE* 4.7 1.8 - - + -
82C HIS* 1.3 86.9 + - - +
84C GLU* 1.3 60.5 + - - +
85C LYS* 4.2 2.0 + - - +
90C ILE* 4.7 0.7 - - + -
91C VAL 3.5 4.9 - - - -
92C TYR* 3.7 26.7 - - + -
119C VAL* 3.7 20.0 - - + -
120C VAL 4.2 6.7 - - - +
122C PRO* 5.3 6.6 - - + +
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Residues in contact with GLU 84 (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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82C HIS* 3.7 19.4 + - + +
83C ALA* 1.3 76.1 - - - +
85C LYS* 1.3 74.3 + - - +
86C ALA* 3.4 16.0 + - - +
90C ILE* 3.5 7.1 - - - +
91C VAL* 2.7 52.9 + - + +
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Residues in contact with LYS 85 (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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83C ALA 4.2 1.3 + - - +
84C GLU* 1.3 81.7 - - - +
86C ALA* 1.3 65.3 + - - +
89C ASN 4.2 2.9 - - - -
90C ILE* 3.9 19.5 - - + -
118C THR* 5.6 4.0 - - - +
119C VAL* 3.9 36.4 - - + +
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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