Contacts of the strand formed by residues 2047 - 2054 (chain B) 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 VAL2047 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036B LYS 3.5 1.0 - - - +
2037B PHE* 3.5 2.9 - - - -
2038B VAL* 2.9 37.2 + - - +
2040B LEU* 5.6 2.5 - - + +
2043B PHE* 6.4 0.2 - - + -
2045B GLN 4.5 5.2 - - - +
2046B PRO* 1.3 72.1 - - - +
2048B ALA* 1.3 71.4 + - - +
2049B ILE* 3.6 14.6 + - + +
2122B TYR* 4.3 9.6 - - + -
2123B THR 3.6 20.0 - - - +
2124B PRO* 4.2 14.6 - - + -
2155B LEU* 3.6 26.7 - - + +
2158B ALA* 4.7 3.6 - - + -
2159B ALA* 4.0 22.7 - - + +
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Residues in contact with ALA2048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024B PRO* 4.1 4.5 - - + -
2036B LYS 3.6 5.2 - - - -
2037B PHE* 3.9 21.1 - - + -
2046B PRO 3.7 2.6 + - - -
2047B VAL* 1.3 70.7 - - - +
2049B ILE* 1.3 60.3 + - - +
2050B PHE* 3.7 21.1 - - + -
2121B ILE 3.6 2.3 - - - +
2122B TYR* 3.7 1.2 - - - -
2123B THR* 2.9 47.3 + - + +
2125B ALA 5.3 2.0 - - - +
2127B LEU* 4.1 12.6 - - + -
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Residues in contact with ILE2049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2035B GLY* 3.2 4.5 - - - -
2036B LYS* 2.8 56.8 + - + +
2038B VAL* 3.7 29.8 - - + -
2047B VAL* 3.9 15.7 - - + +
2048B ALA* 1.3 77.2 - - - +
2050B PHE* 1.3 66.4 - - - +
2051B LEU* 3.7 29.6 - - + -
2080B ALA 4.2 1.2 - - - +
2121B ILE 3.3 4.3 - - - +
2122B TYR* 3.7 35.0 - - + -
2153B ASP* 5.1 0.9 - - - +
2155B LEU* 4.7 8.7 - - + -
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Residues in contact with PHE2050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024B PRO* 3.9 25.1 - - + -
2026B VAL* 3.6 28.7 - - + -
2033B VAL* 3.7 22.7 - - + -
2034B LEU 4.1 1.8 - - - -
2035B GLY* 3.5 28.5 - - - -
2048B ALA* 3.7 28.7 - - + -
2049B ILE* 1.3 73.0 - - - +
2051B LEU* 1.3 64.0 + - - +
2053B ILE* 3.7 20.8 - - + +
2080B ALA* 3.6 6.1 - - + -
2119B LEU 4.2 1.4 - - - +
2120B ASN* 3.3 5.2 - - - +
2121B ILE* 2.8 45.2 + - + +
2123B THR* 4.2 4.0 - - + -
2127B LEU* 4.2 0.9 - - + -
2208B PHE* 3.8 23.3 - + - -
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Residues in contact with LEU2051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036B LYS* 4.1 14.4 - - - +
2049B ILE* 3.7 24.9 - - + -
2050B PHE* 1.3 74.4 - - - +
2052B GLY* 1.3 65.8 + - - +
2053B ILE 3.6 0.9 - - - -
2079B ASN 4.8 0.2 - - - +
2080B ALA* 2.8 36.5 + - - +
2081B THR* 3.9 18.8 - - - +
2082B SER 3.5 17.0 - - - +
2083B TYR* 3.4 49.6 - - + +
2120B ASN* 3.4 26.2 - - + +
2122B TYR* 3.9 6.7 - - + +
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Residues in contact with GLY2052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2051B LEU* 1.3 73.8 - - - +
2053B ILE* 1.3 61.1 + - - +
2054B PRO* 3.5 5.9 - - - +
2078B LYS* 4.9 4.9 - - - +
2079B ASN 5.6 0.7 - - - +
2080B ALA* 5.1 2.2 - - - +
2082B SER 4.3 2.7 - - - -
2084B PRO* 3.9 19.8 - - - +
2118B TYR* 3.2 29.3 - - - -
2119B LEU 3.7 0.4 + - - -
2120B ASN* 2.9 16.5 + - - -
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Residues in contact with ILE2053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2028B THR* 5.7 0.2 - - + -
2033B VAL* 4.5 20.0 - - + -
2050B PHE* 3.7 31.0 - - + +
2052B GLY* 1.3 74.5 - - - +
2054B PRO* 1.3 78.1 - - + +
2055B PHE 3.5 0.5 + - - -
2074B TRP* 5.0 4.7 - - + -
2078B LYS* 5.5 1.1 - - + -
2080B ALA* 4.3 11.7 - - + -
2118B TYR* 3.3 1.9 - - - -
2119B LEU* 3.0 40.8 + - + +
2121B ILE* 3.9 24.5 - - + -
2200B TRP* 3.6 26.2 - - + +
2208B PHE* 3.9 14.6 - - + -
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Residues in contact with PRO2054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2030B HIS* 5.5 0.3 - - - -
2052B GLY 3.5 8.7 - - - +
2053B ILE* 1.3 96.0 - - + +
2055B PHE* 1.3 61.3 + - - +
2056B ALA 3.5 13.0 - - - +
2058B PRO* 6.3 1.8 - - + -
2071B ALA* 4.1 13.2 - - + +
2074B TRP* 4.0 24.0 - - + -
2078B LYS* 4.0 23.8 - - + +
2117B LEU 3.6 8.5 - - - +
2118B TYR* 3.7 18.8 - - + +
2200B TRP* 4.0 7.4 + - - -
3183C GLU* 4.8 4.5 - - - +
3184C HIS* 6.2 3.8 - - + +
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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