Contacts of the strand formed by residues 3214 - 3217 (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 GLU3214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3079D TYR* 4.2 5.2 - - - -
3080D THR* 4.6 2.2 - - - +
3174D SER* 2.6 33.6 + - - -
3175D THR 3.2 15.0 - - - +
3176D SER* 4.9 0.2 - - - -
3202D TYR* 3.5 5.8 - - - -
3203D ILE* 3.1 53.7 + - + +
3204D ASP* 3.6 5.1 + - - +
3209D PHE 4.9 0.2 - - - +
3210D ALA* 3.4 10.8 - - + +
3211D GLY* 2.6 47.9 + - - +
3212D GLN 3.0 2.4 - - - -
3213D LEU* 1.3 77.2 - - - +
3215D MET* 1.3 66.8 + - - +
3216D LEU* 4.0 1.4 - - - +
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Residues in contact with MET3215 (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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3058D TRP* 3.6 30.7 - - + -
3062D GLN* 5.7 0.9 - - + -
3066D TYR* 5.2 1.8 - - - +
3120D THR* 4.7 4.0 - - - -
3124D ILE* 3.8 18.6 - - + -
3126D LEU* 4.0 24.2 - - + -
3173D ILE 3.8 0.9 - - - +
3175D THR* 2.8 51.2 + - - +
3176D SER 4.9 0.2 - - - +
3177D LEU* 3.9 11.7 - - + -
3200D ALA* 4.3 22.0 - - + +
3201D GLY 3.2 6.5 - - - +
3202D TYR* 3.6 34.3 - - + +
3213D LEU 3.3 4.2 + - - +
3214D GLU* 1.3 74.1 - - - +
3216D LEU* 1.3 61.9 + - - +
3217D LEU* 4.6 0.7 - - - +
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Residues in contact with LEU3216 (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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3076D ILE* 5.5 1.8 - - + -
3079D TYR* 3.6 42.8 - - + +
3111D LEU* 4.0 31.9 - - + -
3115D PHE* 3.2 14.9 - - + -
3118D MET* 6.0 0.7 - - + -
3172D TYR* 3.9 10.3 - - + -
3173D ILE 3.7 10.5 - - - +
3174D SER* 3.7 14.1 - - - +
3200D ALA* 3.4 3.1 - - - -
3201D GLY* 2.7 38.1 + - - +
3203D ILE* 4.1 25.1 - - + -
3214D GLU* 4.0 3.2 - - - +
3215D MET* 1.3 72.8 - - - +
3217D LEU* 1.3 66.8 + - - +
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Residues in contact with LEU3217 (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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3115D PHE* 3.6 3.9 - - - -
3126D LEU* 3.9 21.3 - - + -
3172D TYR* 3.7 9.9 - - - +
3173D ILE* 2.9 42.5 + - + +
3175D THR* 4.2 18.4 - - + -
3192D PHE* 4.9 2.2 - - + -
3194D VAL* 4.6 10.5 - - + -
3199D LYS 3.6 8.1 - - - +
3200D ALA* 3.5 30.3 - - + -
3215D MET* 4.6 1.1 - - + +
3216D LEU* 1.3 75.8 - - - +
3218D PRO* 1.3 75.0 - - + +
3221D SER* 5.2 1.8 - - - +
3243D MET* 3.7 34.3 - - + -
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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