Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 2Q2L
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 GLY 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 1.3 75.3 - - - +
41A LEU* 1.3 70.8 + - - -
42A HIS* 3.2 13.2 + - - -
86A ILE 3.7 0.3 - - - +
87A THR* 4.5 3.1 - - - -
88A VAL 2.8 35.1 + - - -
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Residues in contact with LEU 41 (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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40A GLY* 1.3 79.1 - - - -
42A HIS* 1.3 64.6 + - - +
85A ASN* 4.0 28.3 - - + +
86A ILE 3.4 4.7 - - - -
87A THR* 4.4 22.0 - - + +
120A ALA 4.6 0.2 - - - +
121A ASP* 3.6 1.9 - - - -
122A PRO* 3.2 44.3 - - + +
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Residues in contact with HIS 42 (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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37A LEU* 3.8 29.5 - - + +
38A LYS* 2.5 44.5 + - + +
39A PRO 4.5 0.9 - - - -
40A GLY 3.2 19.9 + - - -
41A LEU* 1.3 76.0 - - - +
43A GLY* 1.3 62.2 + - - +
85A ASN* 3.1 4.9 - - - -
86A ILE* 2.8 48.6 + - + +
88A VAL* 3.5 8.2 - - + +
118A VAL* 4.2 7.2 - - + -
119A HIS 2.9 24.2 - - - +
120A ALA* 3.2 21.9 + - - -
121A ASP 3.6 2.9 - - - -
143A ILE* 5.1 1.0 - - + +
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Residues in contact with GLY 43 (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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42A HIS* 1.3 74.0 - - - +
44A PHE* 1.3 60.8 + - - +
45A HIS* 3.6 12.6 - - - -
84A GLY 3.3 9.0 - - - -
85A ASN* 3.2 8.9 - - - +
118A VAL* 3.7 3.3 - - - +
119A HIS* 3.1 28.2 + - - +
121A ASP 2.9 16.4 + - - -
123A ASP* 3.8 12.6 - - - -
139A ALA* 4.3 2.2 - - - -
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Residues in contact with PHE 44 (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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8A LEU* 5.8 1.1 - - + -
18A ILE* 4.1 21.1 - - + -
30A VAL* 4.3 9.2 - - + -
34A ILE* 4.5 5.8 - - + -
42A HIS 4.2 2.5 - - - +
43A GLY* 1.3 75.6 - - - -
45A HIS* 1.3 65.8 + - - +
83A LEU* 2.8 44.3 - - + +
84A GLY 2.9 13.2 + - - +
85A ASN 4.7 0.2 - - - -
86A ILE* 4.0 26.2 - - + +
96A PHE* 3.8 29.8 - + - -
98A ILE* 4.1 17.7 - - + -
116A VAL* 3.5 32.8 - - + -
117A VAL 3.6 12.6 - - - -
118A VAL* 4.2 15.9 - - + -
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Residues in contact with HIS 45 (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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43A GLY* 3.6 7.2 - - - -
44A PHE* 1.3 98.3 + - - +
46A VAL* 1.3 64.8 + - - +
47A HIS* 3.8 6.5 + - + -
62A HIS* 3.3 43.7 + + + -
70A HIS* 4.3 2.9 - + - -
81A GLY 3.2 9.9 - - - +
82A ASP* 4.3 1.1 - - - -
83A LEU* 4.2 13.0 - - - -
84A GLY 4.0 1.1 + - - -
116A VAL* 3.4 7.3 - - - +
117A VAL 3.0 30.9 + - - -
119A HIS* 3.2 32.5 + + - -
123A ASP* 2.8 28.3 + - - -
136A THR 4.2 0.4 - - - -
139A ALA* 4.2 11.2 - - + -
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Residues in contact with VAL 46 (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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20A PHE* 4.7 3.1 - - + -
45A HIS* 1.3 74.2 - - - +
47A HIS* 1.3 69.4 + - - +
62A HIS* 3.7 4.2 - - - +
63A PHE* 2.8 26.8 + - + +
81A GLY* 3.0 21.8 + - - +
83A LEU* 3.6 24.0 - - + +
103A ILE* 4.1 17.7 - - + -
111A ILE* 3.8 29.2 - - + -
114A ARG* 4.4 3.6 - - + -
115A ALA 3.5 10.8 - - - +
116A VAL* 4.1 12.8 - - + +
148A ILE* 4.2 11.4 - - + -
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Residues in contact with HIS 47 (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 HIS* 3.9 11.6 - - + +
46A VAL* 1.3 82.4 - - - +
48A ALA* 1.3 65.9 + - - +
49A LEU 3.5 1.1 - - - -
59A THR* 3.5 19.3 - - - +
60A GLY 2.8 22.8 + - - -
61A PRO* 3.4 6.3 + - + -
62A HIS* 3.3 22.1 - + - -
63A PHE* 3.8 4.0 - - - +
114A ARG* 3.6 13.3 - - - +
115A ALA 2.7 20.1 + - - +
117A VAL* 3.5 23.3 - - + +
119A HIS* 3.2 31.4 - + - -
142A ARG* 3.5 23.8 + - - -
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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