Contacts of the strand formed by residues 3188 - 3194 (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 ILE3188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3129D GLY* 3.3 5.7 - - - -
3130D ASP* 2.9 37.6 + - + +
3131D ASP 3.7 21.5 - - - +
3134D TYR* 4.2 12.1 - - + -
3135D LEU* 3.6 35.7 - - + -
3143D LEU* 3.9 11.7 - - + -
3186D ARG* 3.2 1.1 - - - +
3187D PRO* 1.3 88.9 - - + +
3189D ILE* 1.3 67.4 + - - +
3190D THR* 4.2 6.9 + - - +
3237D ILE* 3.5 14.8 - - + +
3239D ILE* 3.7 28.9 - - + -
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Residues in contact with ILE3189 (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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3127D PHE* 4.7 11.2 - - + -
3128D ARG 3.6 6.3 - - - +
3129D GLY* 4.3 7.9 - - - -
3179D ASN* 4.4 26.5 - - - +
3183D PHE* 3.6 22.0 - - + +
3186D ARG* 4.0 4.0 - - + +
3188D ILE* 1.3 83.6 - - - +
3190D THR* 1.3 69.7 + - - +
3191D LYS* 4.7 7.9 - - + -
3236D GLN* 3.4 36.6 - - + +
3237D ILE 2.8 9.5 + - - +
3238D ILE* 3.4 21.8 - - + +
3239D ILE* 2.8 27.7 + - - +
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Residues in contact with THR3190 (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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3126D LEU 3.6 0.7 - - - +
3127D PHE* 3.3 8.1 - - - +
3128D ARG* 2.9 44.0 + - - +
3130D ASP* 4.6 7.1 + - - -
3134D TYR* 4.7 11.0 + - - +
3188D ILE* 4.2 5.4 + - - +
3189D ILE* 1.3 75.6 - - - +
3191D LYS* 1.3 66.6 + - - +
3192D PHE* 3.5 39.6 - - + -
3223D TYR* 5.7 0.2 - - + -
3239D ILE* 3.2 32.7 - - + +
3241D ALA* 4.9 2.9 - - + -
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Residues in contact with LYS3191 (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* 5.2 7.1 + - - +
3125D MET* 3.5 20.0 - - + -
3126D LEU 3.4 5.8 - - - +
3127D PHE* 3.7 32.3 - - + -
3179D ASN* 6.0 2.0 - - - +
3189D ILE* 4.7 8.3 - - + -
3190D THR* 1.3 74.9 - - - +
3192D PHE* 1.3 63.3 - - - +
3193D LYS 4.0 0.2 + - - -
3238D ILE* 3.9 28.9 - - + +
3239D ILE 2.7 14.2 + - - +
3240D THR* 3.4 14.2 - - + +
3241D ALA 2.9 26.0 + - - +
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Residues in contact with PHE3192 (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 3.5 1.7 - - - +
3125D MET* 3.3 7.7 - - - +
3126D LEU* 2.8 43.0 + - + +
3128D ARG* 3.9 26.2 - - + -
3134D TYR* 5.6 0.9 - + - -
3173D ILE* 4.0 17.9 - - + -
3175D THR* 4.1 14.1 - - + -
3190D THR* 3.5 30.5 - - + -
3191D LYS* 1.3 73.2 - - - +
3193D LYS* 1.3 61.8 + - - +
3194D VAL* 3.6 15.5 + - + +
3217D LEU* 4.9 0.7 - - + -
3223D TYR* 3.7 46.4 - + + -
3241D ALA* 3.4 13.0 - - + -
3243D MET* 3.5 21.5 - - + -
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Residues in contact with LYS3193 (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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3043D SER* 6.0 4.0 - - - -
3044D ASN 5.0 5.1 + - - -
3046D TYR* 3.6 40.6 + - + +
3124D ILE 3.9 3.4 - - - -
3125D MET* 3.5 26.2 - - + -
3192D PHE* 1.3 71.6 - - - +
3194D VAL* 1.3 60.1 + - - +
3195D ALA 4.0 1.0 + - - -
3226D ASP* 4.9 3.9 + - - +
3240D THR* 4.0 22.7 - - + +
3241D ALA 2.7 17.2 + - - +
3242D THR* 3.9 19.5 - - - +
3243D MET* 3.0 24.5 + - - +
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Residues in contact with VAL3194 (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* 3.4 3.2 - - - -
3120D THR* 4.1 10.8 - - + -
3122D GLU 3.8 1.0 - - - +
3123D ASN* 3.2 2.6 - - - -
3124D ILE* 2.8 48.5 + - + +
3126D LEU* 3.7 27.6 - - + -
3192D PHE* 4.2 10.5 - - + +
3193D LYS* 1.3 75.7 - - - +
3195D ALA* 1.3 61.4 + - - +
3198D SER* 3.5 28.9 - - - +
3200D ALA* 4.8 10.3 - - + -
3217D LEU* 4.6 7.6 - - + -
3243D MET* 4.0 23.3 - - + -
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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