Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 1Q90
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 VAL 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A THR* 1.3 86.2 - - - +
45A PHE* 1.3 62.7 + - - +
84A ALA* 3.6 31.4 - - + -
88A ARG* 3.8 29.6 - - + +
89A VAL* 4.8 1.1 - - + -
90A PRO* 4.6 17.4 - - + +
93A ILE* 4.6 13.4 - - + +
129A PRO* 4.3 10.3 - - + -
130A ILE 2.9 13.0 - - - +
131A LEU* 3.9 12.8 - - + -
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Residues in contact with PHE 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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35A VAL* 4.5 10.3 - - + -
36A PRO* 3.7 33.4 - - + -
39A VAL* 3.8 27.1 - - + -
43A THR* 3.9 3.8 - - + -
44A VAL* 1.3 76.2 - - - +
46A GLU* 1.3 63.4 + - - +
77A LEU* 5.9 0.2 - - + -
81A PHE* 3.7 24.7 - + - -
93A ILE* 6.0 0.2 - - - -
128A VAL 3.8 0.2 - - - +
129A PRO* 3.6 2.1 - - - +
130A ILE* 2.7 80.5 + - + +
132A SER* 3.8 17.7 - - - -
148A ILE* 5.0 6.1 - - + -
244A ILE* 4.3 17.5 - - + -
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Residues in contact with GLU 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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34A GLU 3.8 6.4 - - - +
35A VAL* 4.2 7.8 - - - -
36A PRO* 4.2 5.6 - - + +
45A PHE* 1.3 84.0 - - - +
47A ALA* 1.3 62.2 + - - +
48A VAL* 3.7 15.7 + - + +
93A ILE* 3.7 32.5 - - + +
96A LYS* 3.2 36.9 + - - +
127A VAL* 3.9 22.5 - - + +
128A VAL 3.4 8.5 - - - +
129A PRO* 4.8 2.2 - - + -
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Residues in contact with ALA 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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33A ILE* 4.6 7.6 - - + -
34A GLU 3.7 5.8 - - - -
35A VAL* 3.8 16.2 - - + -
45A PHE 4.3 0.4 + - - -
46A GLU* 1.3 70.5 - - - +
48A VAL* 1.3 61.4 + - - +
49A ILE* 3.9 3.6 + - + -
75A LEU* 4.1 11.7 - - + -
127A VAL* 3.5 2.6 - - - -
128A VAL* 2.8 42.7 + - + +
130A ILE* 3.6 26.3 - - + +
148A ILE* 6.2 0.4 - - + -
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Residues in contact with VAL 48 (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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32A GLU* 4.2 1.6 - - - +
33A ILE* 3.1 3.8 + - - -
34A GLU* 2.9 46.1 + - + +
46A GLU* 4.2 19.3 - - + +
47A ALA* 1.3 75.3 - - - +
49A ILE* 1.3 66.5 + - - +
50A GLU* 5.0 12.5 - - + +
96A LYS* 5.4 3.8 - - - +
125A GLU* 6.3 0.9 - - + -
126A MET 3.7 8.7 - - - +
127A VAL* 4.1 17.7 - - + -
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Residues in contact with ILE 49 (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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32A GLU 3.3 5.8 - - - +
33A ILE* 3.5 27.1 - - + -
47A ALA* 4.7 5.8 - - + +
48A VAL* 1.3 76.7 - - - +
50A GLU* 1.3 66.4 + - - +
51A LEU* 4.3 3.6 - - + -
73A MET* 3.7 20.9 - - + -
75A LEU* 5.5 1.6 - - + -
125A GLU* 3.3 3.6 - - - +
126A MET* 2.9 64.9 + - + +
128A VAL* 4.4 12.8 - - + -
150A PHE* 3.4 41.1 - - + -
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Residues in contact with GLU 50 (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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31A VAL* 3.3 9.7 - - - +
32A GLU* 2.9 58.2 + - + +
48A VAL* 5.0 11.6 - - + +
49A ILE* 1.3 79.6 - - - +
51A LEU* 1.3 62.8 + - - +
52A PRO* 3.3 10.9 - - + +
124A SER 3.6 5.2 - - - +
125A GLU* 3.7 27.6 - - + +
150A PHE* 4.6 0.2 - - - -
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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