Contacts of the strand formed by residues 2204 - 2210 (chain A) in PDB entry 5W0P
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 LEU2204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2194A SER* 3.4 3.3 - - - -
2195A TRP* 2.9 58.9 + - + +
2197A PHE* 5.5 10.1 - - + -
2203A PRO* 1.3 75.5 - - - +
2205A ASN* 1.3 65.1 + - - +
2206A LEU* 5.9 0.9 - - + -
2227A VAL* 4.5 10.5 - - + -
2228A THR 3.3 21.1 - - - +
2229A ASN* 3.7 25.1 - - + +
2231A THR* 4.3 15.7 - - + -
2235A VAL* 5.2 5.2 - - + -
2334A LEU* 4.6 20.2 - - + -
2336A VAL* 4.9 15.3 - - + -
2348A VAL* 5.8 4.5 - - + -
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Residues in contact with ASN2205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192A GLU* 5.7 7.4 - - + +
2193A ALA 3.8 3.1 - - - +
2194A SER* 3.2 26.0 - - - -
2203A PRO* 4.2 8.0 - - - +
2204A LEU* 1.3 77.6 - - - +
2206A LEU* 1.3 62.7 + - - +
2226A THR 4.6 0.2 - - - -
2227A VAL* 3.9 1.0 - - - +
2228A THR* 2.9 50.9 + - + +
2230A ASN* 4.5 15.3 - - - +
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Residues in contact with LEU2206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2191A ALA 5.5 0.2 - - - +
2192A GLU* 3.5 7.1 - - - +
2193A ALA 3.0 37.8 + - - +
2195A TRP* 4.5 12.6 - - + +
2204A LEU* 5.9 1.1 - - + -
2205A ASN* 1.3 76.4 - - - +
2207A SER* 1.3 63.1 + - - +
2208A VAL* 3.5 31.0 - - + +
2225A VAL* 4.1 11.0 - - + -
2226A THR 3.4 8.7 - - - +
2227A VAL* 4.0 19.7 - - + -
2332A VAL* 4.5 6.1 - - + +
2334A LEU* 3.4 36.3 - - + -
2350A THR* 3.8 18.8 - - + -
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Residues in contact with SER2207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190A SER* 4.5 6.9 + - - -
2191A ALA 3.5 9.0 + - - -
2192A GLU* 4.3 17.8 - - - +
2206A LEU* 1.3 77.0 - - - +
2208A VAL* 1.3 66.6 + - - +
2209A SER* 5.2 2.6 - - - -
2224A THR 3.7 0.7 - - - +
2225A VAL* 3.7 1.2 - - - -
2226A THR* 2.9 47.4 + - - -
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Residues in contact with VAL2208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190A SER* 3.5 5.7 + - - -
2191A ALA* 2.8 43.1 + - + +
2206A LEU* 3.5 24.7 - - + +
2207A SER* 1.3 74.4 + - - +
2209A SER* 1.3 67.8 + - - +
2210A LEU* 4.9 1.6 - - + -
2223A VAL* 3.9 26.7 - - + -
2224A THR 3.4 3.8 - - - +
2225A VAL* 4.7 3.1 - - + +
2330A ILE* 5.2 0.2 - - + -
2332A VAL* 3.7 21.8 - - + -
2350A THR* 3.9 13.7 - - + +
2352A VAL* 4.2 21.3 - - + -
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Residues in contact with SER2209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2188A GLN* 4.1 12.3 + - - +
2189A PRO 3.5 9.8 + - - -
2190A SER* 5.0 6.4 - - - -
2207A SER* 5.2 2.9 - - - -
2208A VAL* 1.3 77.4 - - - +
2210A LEU* 1.3 72.4 + - - +
2223A VAL 3.8 0.5 - - - -
2224A THR* 2.7 57.8 + - - -
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Residues in contact with LEU2210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2188A GLN* 3.1 28.9 + - - +
2189A PRO* 3.0 41.1 + - + -
2208A VAL* 4.9 2.7 - - + -
2209A SER* 1.3 78.0 + - - +
2211A SER* 1.3 60.3 + - - +
2212A LYS 3.9 4.5 - - - +
2215A TYR* 3.9 10.5 - - + +
2221A ILE* 4.5 3.1 - - + -
2222A PRO 3.3 19.5 - - - +
2223A VAL* 3.8 28.7 - - + -
2224A THR* 5.6 1.3 - - - -
2330A ILE* 4.3 18.8 - - + -
2352A VAL* 4.6 12.1 - - + -
2353A PRO 4.8 1.1 - - - +
2354A PHE* 4.2 22.2 - - + -
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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