Contacts of the strand formed by residues 3133 - 3139 (chain C) in PDB entry 2H7C
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 LEU3133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3124C PRO* 3.8 20.2 - - + -
3125C ALA* 3.6 27.4 - - + +
3131C ASN* 4.3 15.9 - - + +
3132C ARG* 1.3 78.4 - - - +
3134C PRO* 1.3 79.4 - - + +
3162C ASN* 3.6 38.4 - - + +
3164C VAL* 4.2 6.5 - - + +
3209C GLY 3.0 14.3 + - - +
3210C GLY* 3.4 3.8 - - - -
3211C ASN* 2.8 22.9 + - - -
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Residues in contact with PRO3134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3132C ARG 3.8 3.6 - - - +
3133C LEU* 1.3 92.2 - - + +
3135C VAL* 1.3 60.0 + - - +
3136C MET* 5.4 0.2 - - - -
3162C ASN 4.4 4.3 - - - +
3163C VAL* 3.7 23.3 - - + +
3164C VAL 3.0 23.4 + - - -
3211C ASN* 4.9 0.2 - - + -
3214C SER* 3.7 26.5 - - - +
3504C ALA* 4.3 18.6 - - + +
3505C ARG* 4.0 28.0 - - + +
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Residues in contact with VAL3135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3133C LEU 3.8 1.3 - - - +
3134C PRO* 1.3 78.5 - - - +
3136C MET* 1.3 61.3 + - - +
3137C VAL* 4.0 14.6 - - + -
3164C VAL* 3.5 11.9 - - + +
3166C VAL* 4.0 22.2 - - + -
3201C VAL* 4.3 5.6 - - + -
3205C ILE* 3.6 31.2 - - + -
3210C GLY* 3.9 2.9 - - - -
3211C ASN 3.7 26.5 - - - +
3214C SER 2.9 11.3 + - - +
3215C VAL* 3.5 7.3 - - + -
3216C THR* 2.7 35.0 + - - +
3504C ALA* 5.1 0.7 - - - +
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Residues in contact with MET3136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135C VAL* 1.3 76.6 - - - +
3137C VAL* 1.3 62.9 + - - +
3138C TRP 3.9 0.3 + - - -
3157C LEU* 4.3 11.4 - - + -
3163C VAL* 4.1 25.6 - - + -
3164C VAL 2.9 12.2 + - - +
3165C VAL* 3.5 11.0 - - + +
3166C VAL 2.9 26.2 + - - +
3216C THR* 3.4 10.3 - - + +
3218C PHE* 3.7 34.1 - - + -
3244C ILE* 4.4 8.7 - - + -
3500C TRP* 3.9 32.8 - - + +
3501C ALA* 4.4 9.4 - - - -
3504C ALA* 3.9 23.6 - - + -
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Residues in contact with VAL3137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135C VAL* 4.0 12.6 - - + -
3136C MET* 1.3 73.7 - - - +
3138C TRP* 1.3 61.4 + - - +
3139C ILE* 3.9 3.0 + - + +
3166C VAL* 3.3 13.2 - - + +
3168C ILE* 3.6 37.9 - - + -
3198C LEU* 4.1 25.4 - - + -
3201C VAL* 4.3 10.3 - - + -
3215C VAL* 3.9 24.9 - - + -
3216C THR 2.8 11.6 + - - +
3217C ILE* 3.5 6.7 - - + +
3218C PHE* 2.9 29.0 + - - +
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Residues in contact with TRP3138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3137C VAL* 1.3 71.2 - - - +
3139C ILE* 1.3 67.7 + - - +
3140C HIS* 3.5 21.5 + - + +
3149C ALA* 5.7 0.9 - - - -
3152C TYR* 3.5 39.0 - + + -
3165C VAL* 5.3 1.1 - - + -
3166C VAL 2.7 14.3 + - - +
3167C THR* 4.1 14.1 - - + -
3168C ILE* 3.3 29.2 + - - +
3218C PHE* 3.2 59.3 - + + -
3219C GLY* 3.4 12.8 - - - -
3220C GLU* 3.5 26.7 - - + -
3246C GLU* 3.7 8.3 - - - -
3472C LEU* 3.4 34.1 - - + -
3475C VAL* 5.1 0.2 - - + -
3476C PHE* 3.3 21.3 - + + -
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Residues in contact with ILE3139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3137C VAL* 4.5 6.1 - - + +
3138C TRP* 1.3 77.8 - - - +
3140C HIS* 1.3 64.7 + - - +
3168C ILE* 4.0 19.1 - - + -
3170C TYR* 3.7 13.0 - - + -
3194C GLN* 3.4 31.0 - - + +
3198C LEU* 6.0 0.9 - - + -
3217C ILE* 4.8 7.6 - - + -
3218C PHE 2.9 14.4 + - - +
3219C GLY* 3.2 20.1 - - - -
3220C GLU 3.8 1.0 + - - -
3223C GLY* 3.2 21.2 - - - +
3226C SER* 4.0 7.4 - - - -
3227C VAL* 3.9 19.5 - - + -
3230C LEU* 3.9 28.3 - - + -
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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