Contacts of the strand formed by residues 29 - 34 (chain U) in PDB entry 5GAD
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 THR 29 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341A G 4.5 8.9 + - - +
1399A C 5.7 0.3 + - - -
20U ALA 4.3 1.9 - - - +
23U ALA* 3.3 24.9 + - + +
24U MET* 3.0 29.0 + - - +
27U SER* 3.8 13.3 + - - -
28U ASN* 1.3 78.0 + - - +
30U ILE* 1.3 71.3 + - - +
31U VAL* 4.7 0.7 - - + +
84U TYR* 4.1 16.2 - - + -
85U VAL 3.2 27.8 - - - +
86U THR* 3.5 19.7 + - - +
87U LEU 4.7 0.2 - - - +
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Residues in contact with ILE 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U MET* 4.5 16.8 - - + -
29U THR* 1.3 79.3 - - - +
31U VAL* 1.3 64.4 + - - +
32U LEU* 4.5 20.2 - - + -
47U VAL* 4.5 19.7 - - + -
51U PHE* 4.6 13.2 - - + -
83U ALA 3.4 2.1 - - - +
84U TYR* 3.7 0.9 - - - -
85U VAL* 2.9 53.4 + - + +
87U LEU* 3.7 26.0 - - + -
93U LEU* 4.7 14.6 - - + +
95U PHE* 6.1 5.4 - - + -
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Residues in contact with VAL 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A G 5.8 0.2 - - - +
14U PRO* 3.8 1.0 - - - +
15U HIS* 2.8 51.4 + - + +
20U ALA* 3.8 33.7 - - + +
23U ALA* 5.4 1.6 - - + -
29U THR* 4.7 2.9 - - + +
30U ILE* 1.3 81.0 - - - +
32U LEU* 1.3 70.5 + - - +
82U LYS* 3.9 23.6 - - + -
83U ALA 3.4 3.4 - - - +
84U TYR* 3.7 31.2 - - + -
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Residues in contact with LEU 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU* 3.6 34.1 - - + -
13U ALA 3.6 12.8 - - - +
14U PRO* 4.1 9.9 - - + -
15U HIS* 4.7 2.7 - - - -
30U ILE* 4.5 19.3 - - + -
31U VAL* 1.3 91.4 - - - +
33U LYS* 1.3 63.7 + - - +
34U VAL* 3.6 14.2 + - + +
43U ILE* 5.1 0.4 - - + -
47U VAL* 4.4 16.2 - - + -
51U PHE* 5.1 11.2 - - + -
81U LYS 3.6 0.5 - - - +
82U LYS* 3.4 6.3 - - - -
83U ALA* 2.9 40.9 + - + +
85U VAL* 4.5 7.4 - - + -
30Z MET* 6.5 0.9 - - + -
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Residues in contact with LYS 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1338A G 5.3 4.0 + - - -
11U LEU* 4.0 0.3 - - - -
12U ARG* 2.9 34.7 + - + +
13U ALA* 2.9 25.9 + - + +
14U PRO 4.7 3.6 - - - -
15U HIS* 3.4 38.7 + - + +
16U VAL* 6.3 0.4 - - - -
32U LEU* 1.3 72.2 - - - +
34U VAL* 1.3 63.4 + - - +
80U TRP* 3.7 43.7 - - + -
81U LYS 3.5 5.2 - - - -
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Residues in contact with VAL 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U VAL* 3.6 14.4 - - + +
11U LEU* 3.8 12.8 - - + -
12U ARG* 4.2 5.8 - - - +
32U LEU* 3.8 23.8 - - + +
33U LYS* 1.3 79.5 - - - +
35U ALA* 1.3 77.1 + - - +
36U LYS 3.4 1.4 + - - -
38U ALA* 4.5 2.7 - - + -
43U ILE* 3.6 34.3 - - + -
80U TRP* 5.1 3.3 - - - +
81U LYS* 2.9 42.0 + - + +
83U ALA* 4.1 4.7 - - + -
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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