Contacts of the strand formed by residues 50 - 54 (chain I) in PDB entry 5GAG
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 50 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I GLY* 2.8 31.7 + - - +
46I ARG* 4.3 6.4 + - - +
48I ALA* 3.4 34.1 - - + +
49I GLY* 1.3 77.5 - - - +
51I TYR* 1.3 62.6 + - - +
52I MET* 4.0 11.8 + - - +
83I ALA* 3.7 30.1 - - + -
84I TYR 3.6 13.5 - - - +
85I VAL* 3.6 12.1 - - + -
86I THR* 5.5 0.4 - - - -
91I ALA 4.1 11.2 - - - +
92I ALA* 4.3 7.2 - - + -
95I LEU* 4.8 3.6 - - + -
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Residues in contact with TYR 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I GLU* 4.2 8.3 + - - +
15I VAL* 4.5 3.6 - - - +
18I VAL* 3.5 40.4 - - + +
50I VAL* 1.3 70.9 - - - +
52I MET* 1.3 59.6 + - - +
53I ARG* 3.0 51.3 + - + -
82I ILE* 3.1 9.8 - - + +
83I ALA* 3.3 1.3 - - - -
84I TYR* 2.8 76.6 + + + +
86I THR* 4.9 5.6 - - + +
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Residues in contact with MET 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A U 5.1 5.1 + - - +
1084A A 2.9 15.1 + - - -
38I MET* 5.3 0.7 - - + -
41I LEU* 3.6 41.5 - - + +
42I ARG* 3.2 31.2 + - - +
45I GLY* 4.2 13.7 - - - -
50I VAL* 4.0 12.5 + - - +
51I TYR* 1.3 74.0 - - - +
53I ARG* 1.3 67.0 + - - +
81I LEU* 4.1 14.8 - - + -
82I ILE 3.5 4.0 - - - -
83I ALA* 4.2 17.5 - - + -
95I LEU* 5.4 2.7 - - - -
96I PHE* 3.6 30.3 - - + -
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Residues in contact with ARG 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A A 3.2 35.7 + - - +
11I ILE* 3.2 25.7 + - - +
14I GLU* 3.9 19.4 + - - +
15I VAL* 3.2 23.3 - - - +
51I TYR* 3.0 40.5 + - + +
52I MET* 1.3 77.3 - - - +
54I VAL* 1.3 57.4 + - - +
55I VAL* 3.4 14.1 + - + +
81I LEU* 3.2 11.0 - - - +
82I ILE* 2.8 60.5 + - + +
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A A 2.6 82.5 + - + +
1106A G 3.9 27.0 - - - +
30I SER* 4.4 14.1 - - - +
38I MET* 4.6 3.8 - - + -
42I ARG* 3.9 7.4 - - - +
53I ARG* 1.3 74.3 + - - +
55I VAL* 1.3 61.0 + - - +
80I THR 3.6 15.3 - - - +
81I LEU* 3.7 20.9 - - + -
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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