Contacts of the strand formed by residues 107 - 111 (chain a) in PDB entry 5A0Q
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 TYR 107 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300Z KNM 5.8 3.1 - - - +
12a ILE* 4.5 3.1 - - - +
54a CYS* 3.6 1.0 - - - -
55a SER* 2.4 59.1 + - - +
56a GLY* 4.2 7.0 - - - -
105a TYR* 3.8 32.1 + + - -
106a VAL* 1.4 68.9 - - - +
108a ASN* 1.3 61.3 + - - +
109a ILE* 5.1 3.1 - - + +
124a PHE 3.7 22.7 - - - +
125a ASP* 4.1 8.3 - - + -
126a PRO* 3.9 21.7 - - + +
138a GLY* 5.2 6.7 - - - -
139a GLY* 4.7 13.2 - - - +
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Residues in contact with ASN 108 (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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52a ILE* 4.3 17.4 - - + +
53a GLY 3.2 8.5 - - - +
54a CYS* 2.6 30.7 - - - +
64a LEU* 3.4 18.4 - - - +
65a THR* 5.4 1.2 - - - +
92a LEU* 4.5 7.6 - - + +
96a LEU* 4.4 6.1 - - - +
106a VAL* 2.3 43.7 - - - +
107a TYR* 1.3 71.9 - - - +
109a ILE* 1.3 63.4 + - - +
110a ILE* 5.3 0.2 - - + -
122a TYR 3.3 2.3 - - - +
124a PHE* 3.0 45.7 + - + +
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Residues in contact with ILE 109 (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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12a ILE* 3.5 35.0 - - + -
14a ALA* 3.4 31.0 - - + -
23a VAL* 4.8 4.2 - - + +
51a VAL 4.1 0.2 - - - +
52a ILE* 3.3 5.0 - - - +
53a GLY 2.9 31.3 + - - +
107a TYR* 5.1 2.9 - - + +
108a ASN* 1.3 76.0 - - - +
110a ILE* 1.4 65.2 + - - +
121a VAL* 3.8 13.2 - - + -
122a TYR 3.5 2.0 - - - +
123a SER* 4.0 15.7 - - - -
124a PHE 4.9 1.3 - - - +
136a LYS* 3.9 36.3 - - + +
138a GLY* 4.8 8.3 - - - +
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Residues in contact with ILE 110 (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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23a VAL* 5.0 1.5 - - - +
50a THR* 5.1 4.3 - - + -
51a VAL 3.9 2.2 - - - +
52a ILE* 3.5 35.7 - - + -
68a ILE* 6.0 0.4 - - + -
85a THR* 3.7 26.9 - - + +
88a ILE* 3.8 39.0 - - + -
89a ALA 5.6 0.4 - - - +
92a LEU* 4.1 6.7 - - + -
108a ASN* 5.3 0.4 - - + -
109a ILE* 1.4 74.6 - - - +
111a GLY* 1.3 61.2 + - - +
112a GLY* 4.1 2.7 - - - +
120a ALA 3.4 1.2 - - - +
121a VAL* 3.3 11.3 - - - +
122a TYR* 3.3 32.5 + - + -
124a PHE* 3.8 25.8 - - + -
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Residues in contact with GLY 111 (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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21a ALA* 4.4 8.3 - - - -
23a VAL* 4.5 10.5 - - - +
49a LYS 2.5 24.4 - - - +
50a THR* 4.2 0.2 - - - -
51a VAL* 2.8 26.9 + - - +
110a ILE* 1.3 76.2 - - - +
112a GLY* 1.3 52.4 + - - -
120a ALA 3.7 11.7 - - - -
198a VAL* 3.6 11.9 - - - +
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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