Contacts of the strand formed by residues 73 - 85 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLN* 3.0 38.1 + - - +
45A HIS 3.6 16.4 + - - +
46A ILE* 3.5 25.2 - - + +
47A VAL 3.1 20.3 + - - -
71A ILE* 4.2 6.1 - - - +
72A SER* 1.3 87.3 + - - +
74A VAL* 1.3 63.6 + - - +
129A ALA* 6.3 1.8 - - - +
130A GLY 3.5 5.7 - - - +
131A HIS* 3.5 36.3 + - + +
144A PHE* 5.8 1.6 - - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.3 3.5 - - - +
47A VAL 3.2 14.1 - - - +
49A CYS* 3.8 10.8 - - + -
54A LEU* 3.9 16.8 - - + -
71A ILE* 3.2 31.2 - - + -
72A SER 3.8 7.0 - - - +
73A GLN* 1.3 81.7 - - - +
75A THR* 1.3 66.3 + - - +
128A VAL* 3.6 1.0 - - - +
129A ALA* 3.5 2.6 - - - +
130A GLY 2.9 35.9 + - - +
132A LEU 4.7 0.2 - - - +
141A LEU* 3.5 37.6 - - + +
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Residues in contact with THR 75 (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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46A ILE* 3.5 24.2 - - + -
47A VAL 3.2 4.9 + - - -
48A PRO* 3.4 12.8 - - - +
49A CYS* 2.8 31.7 + - - +
74A VAL* 1.3 78.7 - - - +
76A ILE* 1.3 59.6 + - - +
127A LYS* 4.1 22.2 - - - -
128A VAL 2.9 12.1 - - - +
129A ALA* 4.2 13.0 - - + -
158A HIS* 3.3 16.9 + - - -
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Residues in contact with ILE 76 (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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49A CYS 2.6 31.4 - - - +
50A THR* 3.9 2.2 - - + -
51A ILE* 4.2 19.1 - - + +
54A LEU* 5.0 5.6 - - + -
75A THR* 1.3 74.7 - - - +
77A VAL* 1.3 96.3 + - - +
94A ILE* 5.1 9.2 - - + -
96A ASP* 3.1 28.0 - - + +
104A VAL* 5.8 1.6 - - + -
127A LYS* 3.5 1.8 - - - +
128A VAL* 2.8 42.2 + - + +
141A LEU* 4.0 27.3 - - + +
158A HIS* 3.5 11.4 - - + +
113B TYR* 6.1 0.9 - - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 1.3 93.2 - - - +
78A GLY* 1.3 60.7 + - - +
96A ASP* 3.3 19.2 - - - +
125A TYR* 4.2 8.9 - - + -
126A VAL 3.3 5.6 - - - +
127A LYS* 4.0 21.3 - - + -
149A LEU* 3.5 29.8 - - + -
154A GLU 5.0 1.8 - - - +
155A PHE* 4.1 22.0 - - + -
158A HIS* 3.4 39.5 - - + +
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Residues in contact with GLY 78 (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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77A VAL* 1.3 75.3 - - - +
79A ILE* 1.3 62.2 + - - -
94A ILE* 3.9 16.3 - - - +
95A ASP 3.2 14.1 - - - -
96A ASP* 4.3 1.1 - - - -
124A THR 3.6 0.5 - - - +
125A TYR* 3.4 14.9 - - - -
126A VAL* 2.8 34.6 + - - +
128A VAL* 6.2 0.2 - - - +
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Residues in contact with ILE 79 (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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78A GLY* 1.3 73.8 - - - -
80A ILE* 1.3 77.0 + - - +
81A ARG* 3.2 41.9 + - - +
94A ILE* 3.3 2.8 - - - -
95A ASP* 2.8 46.1 + - - +
97A MET* 5.4 2.5 - - - -
123A GLU* 3.6 27.4 - - - +
124A THR 3.2 11.9 - - - +
125A TYR* 4.4 26.0 - - + +
68B GLU* 5.7 0.9 - - - +
85B VAL* 3.6 26.0 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 1.3 74.0 - - - +
81A ARG* 1.3 57.6 + - - +
82A HIS 3.7 21.3 - - - +
83A ALA* 4.6 1.1 - - + -
92A TYR* 3.6 30.1 - - + -
93A LYS 3.6 4.5 - - - +
94A ILE* 4.1 13.9 - - + -
120A VAL* 3.6 38.6 - - + +
121A PRO 3.8 16.8 - - - +
122A PRO* 3.4 9.0 - - + +
123A GLU* 2.8 28.8 + - - -
124A THR 2.9 10.6 + - - +
126A VAL* 3.6 22.7 - - + -
146A ILE* 4.9 0.4 - - + -
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Residues in contact with ARG 81 (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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79A ILE* 3.5 40.6 - - - +
80A ILE* 1.3 75.3 - - - +
82A HIS* 1.3 64.9 + - + +
93A LYS* 2.8 19.0 + - + +
95A ASP* 3.0 45.6 + - + +
97A MET* 4.2 8.7 - - - -
101A PRO* 4.5 10.5 - - + -
122A PRO* 3.8 13.4 - - - +
123A GLU* 4.7 7.5 + - - +
5B MET* 3.5 35.9 - - - +
9B ARG* 4.1 6.3 - - - +
68B GLU* 5.8 2.0 + - - -
70B VAL* 4.6 8.9 - - - +
83B SER* 4.4 7.1 + - - -
85B VAL* 4.7 4.2 - - - +
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Residues in contact with HIS 82 (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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80A ILE* 3.6 8.6 - - - +
81A ARG* 1.3 81.5 - - + +
83A ALA* 1.3 85.9 + - - +
84A GLU* 4.2 14.2 + - + +
91A VAL 4.5 1.2 + - - -
92A TYR* 3.4 3.8 - - - -
93A LYS* 3.0 46.6 + - + +
122A PRO* 4.9 5.2 - - + -
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Residues in contact with ALA 83 (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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80A ILE* 4.6 2.9 - - + -
82A HIS* 1.3 90.2 + - - +
84A GLU* 1.3 61.3 + - - +
85A LYS* 4.2 2.6 + - - +
90A ILE* 4.9 0.2 - - + -
91A VAL 3.5 4.9 - - - -
92A TYR* 3.6 26.9 - - + -
119A VAL* 3.7 18.6 - - + +
120A VAL 4.4 5.2 - - - +
122A PRO* 5.0 9.3 - - + +
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Residues in contact with GLU 84 (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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82A HIS* 4.2 14.9 + - + +
83A ALA* 1.3 72.4 - - - +
85A LYS* 1.3 77.7 + - - +
86A ALA* 4.0 13.1 - - - +
87A PRO* 5.4 1.0 - - - +
90A ILE* 3.4 10.9 - - - +
91A VAL* 2.8 56.3 + - + +
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Residues in contact with LYS 85 (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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83A ALA 4.2 2.0 + - - +
84A GLU* 1.3 81.8 - - - +
86A ALA* 1.3 65.2 + - - +
89A ASN 4.3 2.7 - - - -
90A ILE* 4.5 7.9 - - + -
119A VAL* 4.4 25.4 - - + -
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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