Contacts of the strand formed by residues 3124 - 3130 (chain D) in PDB entry 1G24
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 ILE3124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3046D TYR* 3.7 4.2 - - - -
3047D GLN* 3.5 11.0 - - + +
3049D PHE* 4.7 14.1 - - + -
3058D TRP* 4.3 11.4 - - + -
3120D THR* 3.4 24.2 - - + +
3122D GLU* 3.4 23.1 - - + +
3123D ASN* 1.3 80.2 - - - +
3125D MET* 1.3 63.5 + - - +
3126D LEU* 3.8 27.1 - - + -
3177D LEU* 4.5 2.5 - - + -
3192D PHE 3.5 1.2 - - - +
3194D VAL* 2.8 48.9 + - + +
3200D ALA* 5.4 0.7 - - + -
3215D MET* 3.8 20.9 - - + -
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Residues in contact with MET3125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3046D TYR* 3.6 22.2 - - + +
3047D GLN 2.9 22.2 + - - +
3048D GLU* 4.1 19.1 - - + +
3049D PHE* 5.5 1.7 - - - -
3124D ILE* 1.3 75.0 - - - +
3126D LEU* 1.3 67.3 + - - +
3127D PHE* 3.9 23.1 - - + -
3177D LEU* 4.0 8.3 - - - +
3191D LYS* 3.5 38.4 - - + +
3192D PHE 3.3 9.2 - - - +
3193D LYS* 3.5 36.8 - - + -
3240D THR* 5.1 2.2 - - + -
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Residues in contact with LEU3126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3124D ILE* 3.8 16.8 - - + -
3125D MET* 1.3 84.4 - - - +
3127D PHE* 1.3 62.1 + - - +
3175D THR* 3.5 26.7 - - + +
3176D SER 3.6 8.1 - - - +
3177D LEU* 3.7 28.3 - - + -
3190D THR 3.6 0.7 - - - +
3191D LYS* 3.4 4.7 - - - +
3192D PHE* 2.8 41.7 + - + +
3194D VAL* 3.7 26.5 - - + -
3200D ALA* 4.9 0.7 - - + -
3215D MET* 4.0 13.0 - - + -
3217D LEU* 3.9 22.7 - - + -
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Residues in contact with PHE3127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3048D GLU* 3.6 36.3 - - + -
3049D PHE 5.5 0.2 - - - -
3125D MET* 3.9 21.3 - - + -
3126D LEU* 1.3 75.4 - - - +
3128D ARG* 1.3 62.3 + - - +
3175D THR* 3.1 7.0 - - - -
3176D SER 2.7 43.1 + - - -
3177D LEU 3.7 14.6 - - - -
3178D MET* 3.7 26.2 - - - +
3179D ASN* 4.0 26.7 - - + +
3183D PHE* 3.6 7.8 - - + -
3189D ILE* 4.7 4.0 - - + -
3190D THR 3.3 5.4 - - - +
3191D LYS* 3.7 46.2 - - + -
3192D PHE* 5.4 0.4 - - - -
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Residues in contact with ARG3128 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3091D ARG* 6.0 2.4 - - - +
3127D PHE* 1.3 79.3 - - - +
3129D GLY* 1.3 69.2 + - - +
3130D ASP* 2.7 36.5 + - - +
3134D TYR* 5.9 1.7 - - - -
3173D ILE* 4.1 10.1 - - - +
3174D SER* 2.6 58.8 + - - +
3175D THR* 4.3 2.0 - - + -
3183D PHE* 3.7 16.4 - - + -
3186D ARG* 5.2 2.0 - - - +
3188D ILE 3.9 0.2 - - - +
3189D ILE* 3.6 5.0 - - - +
3190D THR* 2.9 37.8 + - - +
3192D PHE* 3.9 30.1 - - + -
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Residues in contact with GLY3129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3128D ARG* 1.3 85.2 + - - +
3130D ASP* 1.3 70.4 + - - +
3183D PHE* 3.5 30.3 - - - +
3186D ARG* 3.2 20.7 + - - -
3188D ILE 3.3 9.0 - - - -
3189D ILE* 4.3 3.1 - - - -
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Residues in contact with ASP3130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3128D ARG* 2.7 45.5 + - - +
3129D GLY* 1.3 77.1 - - - +
3131D ASP* 1.3 66.9 + - - +
3134D TYR* 3.6 42.5 - - + +
3186D ARG* 3.6 7.5 - - - +
3187D PRO* 3.4 19.4 - - - +
3188D ILE* 2.9 26.0 + - + +
3190D THR* 4.6 6.8 + - - -
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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