Contacts of the strand formed by residues 2345 - 2357 (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 SER2345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2335A THR* 4.5 16.0 - - - +
2336A VAL 3.2 15.3 - - - -
2337A SER* 4.9 0.7 - - - -
2338A GLY* 3.6 4.9 - - - +
2342A GLU 5.3 1.1 - - - -
2343A LEU 3.6 7.4 + - - -
2344A THR* 1.3 83.9 - - - +
2346A SER* 1.3 60.9 + - - +
2347A GLU* 4.0 9.0 + - - +
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Residues in contact with SER2346 (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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2197A PHE* 3.8 30.2 - - - -
2334A LEU 3.8 0.2 - - - +
2336A VAL* 3.0 36.7 + - - +
2337A SER 5.6 0.4 - - - -
2338A GLY* 4.5 6.0 - - - +
2345A SER* 1.3 72.7 - - - +
2347A GLU* 1.3 63.8 + - - +
2348A VAL* 3.5 15.2 + - - +
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Residues in contact with GLU2347 (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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2333A LYS* 3.4 39.2 + - + -
2334A LEU 3.4 9.0 - - - +
2335A THR* 5.0 13.4 + - + +
2345A SER* 4.0 9.1 + - - +
2346A SER* 1.3 73.2 + - - +
2348A VAL* 1.3 63.3 + - - +
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Residues in contact with VAL2348 (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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2195A TRP* 3.3 55.9 - - + +
2197A PHE* 5.4 7.0 - - + -
2204A LEU* 5.8 4.0 - - + -
2332A VAL 3.9 0.3 - - - +
2333A LYS* 3.6 1.1 - - - +
2334A LEU* 2.6 54.6 + - + +
2336A VAL* 4.9 8.1 - - + -
2346A SER* 3.7 22.2 - - - +
2347A GLU* 1.3 78.7 - - - +
2349A ALA* 1.3 65.0 + - - +
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Residues in contact with ALA2349 (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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2195A TRP* 3.1 22.8 - - - -
2331A LYS* 3.9 25.1 - - + -
2332A VAL 3.3 14.4 - - - +
2333A LYS* 4.0 9.6 - - + -
2334A LEU* 6.2 0.2 - - - -
2348A VAL* 1.3 81.2 - - - +
2350A THR* 1.3 61.6 + - - +
2351A GLU* 5.8 0.4 - - - -
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Residues in contact with THR2350 (chain A).
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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2191A ALA* 4.7 10.2 - - + +
2192A GLU 5.4 1.6 + - - -
2193A ALA* 4.5 11.5 - - + +
2195A TRP* 4.2 13.9 - - + -
2206A LEU* 3.8 29.4 - - + -
2208A VAL* 3.9 14.8 - - + +
2330A ILE 3.6 0.9 - - - +
2331A LYS* 3.5 3.3 - - - -
2332A VAL* 3.2 30.1 + - + +
2349A ALA* 1.3 76.6 - - - +
2351A GLU* 1.3 73.2 + - - +
2352A VAL* 5.8 0.2 - - - +
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Residues in contact with GLU2351 (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* 4.2 7.6 - - - +
2243A GLU* 4.1 5.2 - - - +
2245A ILE* 5.4 2.4 - - - +
2329A HIS* 3.3 42.9 + - + -
2330A ILE 3.5 4.0 - - - -
2331A LYS* 4.3 15.2 - - + +
2349A ALA 5.8 0.2 - - - -
2350A THR* 1.3 87.9 + - - +
2352A VAL* 1.3 62.4 + - - +
2353A PRO* 4.6 1.5 - - - +
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Residues in contact with VAL2352 (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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2189A PRO* 4.0 21.8 - - + -
2190A SER 4.8 2.7 - - - +
2191A ALA* 3.8 22.7 - - + +
2208A VAL* 4.2 23.1 - - + -
2210A LEU* 4.6 9.0 - - + -
2329A HIS* 3.2 3.9 - - - -
2330A ILE* 2.9 49.7 + - + +
2351A GLU* 1.3 77.1 - - - +
2353A PRO* 1.3 83.9 - - + +
2354A PHE* 4.4 0.7 - - - -
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Residues in contact with PRO2353 (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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2189A PRO* 4.6 8.7 - - - +
2213A GLU* 5.2 3.2 - - - +
2327A SER* 5.6 3.4 - - - +
2328A TYR 3.6 11.7 - - - +
2329A HIS* 4.0 4.0 - - + -
2351A GLU 4.6 1.6 - - - +
2352A VAL* 1.3 99.2 - - + +
2354A PHE* 1.3 64.5 + - - +
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Residues in contact with PHE2354 (chain A).
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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2189A PRO* 5.5 0.2 - - + -
2210A LEU* 4.2 14.8 - - + -
2213A GLU* 3.5 18.2 - - - +
2215A TYR* 3.7 15.0 - + + -
2221A ILE* 3.6 25.6 - - + -
2242A VAL* 3.6 22.2 - - + -
2283A PRO* 5.7 0.4 - - + -
2310A SER* 4.2 0.7 + - - -
2327A SER* 5.2 0.3 + - - -
2328A TYR* 3.2 42.1 + + + +
2329A HIS* 3.6 29.2 - - - -
2330A ILE* 3.5 29.8 - - + -
2353A PRO* 1.3 76.8 - - - +
2355A ARG* 1.3 78.2 + - - +
2356A LEU* 4.3 11.7 - - + -
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Residues in contact with ARG2355 (chain A).
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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2182A PRO* 5.6 2.2 - - - +
2213A GLU* 2.8 44.7 + - - +
2214A ILE* 4.0 30.1 - - + +
2215A TYR* 2.8 30.5 + - - -
2310A SER* 3.5 14.8 - - - +
2312A ILE* 4.0 28.5 - - - +
2354A PHE* 1.3 84.6 - - - +
2356A LEU* 1.3 57.3 + - - +
2357A MET* 4.0 22.7 - - + -
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Residues in contact with LEU2356 (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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2215A TYR* 3.5 14.4 - - + +
2216A PHE 3.3 33.9 - - - +
2217A HIS* 3.6 30.9 - - + +
2219A GLU 5.5 0.2 - - - +
2221A ILE* 4.9 1.1 - - + -
2283A PRO* 4.3 33.9 - - + +
2307A LEU* 4.7 3.4 - - + -
2308A ALA 4.2 0.7 - - - +
2309A SER* 3.4 6.6 - - - -
2310A SER* 2.8 32.7 + - - +
2328A TYR* 4.2 29.6 - - + +
2354A PHE* 4.2 13.4 + - + -
2355A ARG* 1.3 73.0 - - - +
2357A MET* 1.3 59.3 + - - +
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Residues in contact with MET2357 (chain A).
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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2179A GLN* 3.3 37.2 - - + +
2180A HIS 3.3 17.7 - - - +
2181A ALA* 3.9 21.8 - - + -
2182A PRO* 4.2 2.9 - - - -
2214A ILE* 5.0 1.3 - - + -
2215A TYR 3.2 7.9 + - - +
2216A PHE* 3.5 19.8 - - - -
2217A HIS* 3.3 19.6 + - - -
2309A SER* 4.2 4.0 - - - -
2310A SER* 3.7 32.1 - - - +
2312A ILE* 3.8 23.8 - - + -
2355A ARG* 4.0 17.0 - - + -
2356A LEU* 1.3 81.1 - - - +
2358A HIS* 1.3 64.6 + - - +
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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