Contacts of the strand formed by residues 2323 - 2337 (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 GLY2323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2066A PHE* 3.6 26.7 - - - -
2084A LEU* 4.6 0.4 - - - -
2128A PRO* 4.0 12.3 - - - -
2146A VAL* 4.4 0.4 - - - -
2247A ASN 3.5 3.6 - - - +
2248A VAL* 3.7 0.2 - - - -
2249A VAL* 2.8 35.2 + - - +
2321A VAL 3.9 1.8 + - - -
2322A MET* 1.3 72.9 - - - +
2324A ILE* 1.3 60.2 + - - -
2325A LEU* 3.6 4.9 + - - +
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Residues in contact with ILE2324 (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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2066A PHE* 3.6 25.3 - - + -
2128A PRO* 4.6 6.5 - - - +
2131A VAL* 3.8 57.8 - - + +
2133A LEU* 4.2 30.5 - - + -
2144A CYS* 5.1 0.2 - - - -
2145A GLY* 4.1 12.8 - - - +
2146A VAL* 3.8 12.9 - - + +
2246A ALA* 4.7 9.4 - - + -
2247A ASN 3.7 2.7 - - - +
2248A VAL* 4.5 17.9 - - + +
2295A ALA* 5.0 0.4 - - + -
2311A THR* 4.2 4.5 - - - +
2323A GLY* 1.3 70.1 - - - -
2325A LEU* 1.3 64.0 + - - +
2326A VAL* 3.9 11.2 + - + -
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Residues in contact with LEU2325 (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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2128A PRO* 4.2 13.0 - - + -
2245A ILE* 3.9 0.9 - - - +
2246A ALA* 4.7 0.2 - - - -
2247A ASN* 2.7 66.9 + - + +
2249A VAL* 4.5 5.4 - - + -
2311A THR* 3.5 17.5 - - - +
2313A ILE* 4.1 26.0 - - + -
2321A VAL* 3.7 42.6 - - + +
2323A GLY 4.2 7.2 - - - +
2324A ILE* 1.3 78.1 - - - +
2326A VAL* 1.3 60.3 + - - +
2327A SER* 4.1 0.7 + - - -
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Residues in contact with VAL2326 (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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2131A VAL* 4.3 11.7 - - + -
2244A GLN* 3.8 28.0 - - + +
2245A ILE 3.4 10.5 - - - +
2246A ALA* 4.6 1.6 - - - +
2295A ALA* 4.2 11.7 - - + -
2308A ALA* 3.8 20.4 - - + -
2309A SER 3.7 13.9 - - - +
2310A SER* 3.9 2.4 - - - -
2311A THR* 3.0 31.6 + - + +
2324A ILE* 3.9 13.9 + - + +
2325A LEU* 1.3 75.8 - - - +
2327A SER* 1.3 65.5 + - - +
2328A TYR* 3.8 18.4 - - + -
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Residues in contact with SER2327 (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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2244A GLN* 3.6 2.8 - - - -
2245A ILE* 2.7 60.5 + - - +
2310A SER* 5.0 3.4 - - - -
2325A LEU 5.3 0.7 - - - -
2326A VAL* 1.3 77.0 - - - +
2328A TYR* 1.3 73.8 + - - +
2353A PRO* 5.6 3.6 - - - +
2354A PHE 5.2 0.3 + - - -
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Residues in contact with TYR2328 (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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2242A VAL* 4.3 14.8 - - + -
2243A GLU 3.6 12.1 - - - -
2244A GLN* 2.8 35.7 + - + -
2245A ILE* 5.3 0.2 - - - -
2260A VAL* 4.5 11.7 - - + -
2307A LEU* 3.7 16.7 - - + +
2308A ALA 2.7 29.5 + - - -
2310A SER* 3.4 21.5 + - - -
2326A VAL* 3.8 13.2 - - + -
2327A SER* 1.3 86.5 + - - +
2329A HIS* 1.3 67.3 + - - +
2353A PRO* 3.6 4.0 - - - +
2354A PHE* 3.2 49.8 + + + +
2356A LEU* 4.2 24.6 - - + +
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Residues in contact with HIS2329 (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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2241A SER 3.7 0.3 - - - +
2242A VAL* 3.8 2.3 - - - -
2243A GLU* 2.9 69.1 + - + +
2245A ILE* 3.3 39.0 - - + +
2257A VAL* 4.4 5.8 - - + -
2328A TYR* 1.3 76.5 - - - +
2330A ILE* 1.3 63.4 + - - +
2331A LYS* 4.2 1.8 - - + -
2351A GLU* 3.3 42.7 + - + -
2352A VAL 3.2 21.1 - - - +
2353A PRO* 4.0 2.9 - - + -
2354A PHE* 3.6 10.1 - - - -
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Residues in contact with ILE2330 (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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2210A LEU* 4.3 19.7 - - + -
2221A ILE* 4.4 13.2 - - + -
2223A VAL* 3.8 19.3 - - + -
2240A VAL* 3.6 27.6 - - + -
2241A SER 3.5 1.1 - - - +
2242A VAL* 3.7 27.8 - - + +
2329A HIS* 1.3 73.9 - - - +
2331A LYS* 1.3 60.9 + - - +
2332A VAL* 3.7 7.2 + - + +
2350A THR 3.6 1.6 - - - +
2351A GLU* 3.5 2.9 - - - -
2352A VAL* 2.9 42.9 + - + +
2354A PHE* 3.5 31.6 - - + -
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Residues in contact with LYS2331 (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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2239A LYS 3.7 0.2 - - - +
2240A VAL 3.6 0.2 - - - -
2241A SER* 2.7 52.6 + - - +
2243A GLU* 2.9 40.1 + - - +
2329A HIS* 3.8 7.4 + - + -
2330A ILE* 1.3 70.4 - - - +
2332A VAL* 1.3 64.7 + - - +
2333A LYS* 3.5 22.9 + - - +
2349A ALA* 3.9 23.8 - - + -
2350A THR 3.5 7.4 - - - +
2351A GLU* 4.3 13.7 - - + +
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Residues in contact with VAL2332 (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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2206A LEU* 4.5 12.6 - - + +
2208A VAL* 3.7 34.5 - - + -
2223A VAL* 4.0 9.9 - - + -
2225A VAL* 4.0 39.3 - - + -
2238A ILE* 4.3 15.9 - - + -
2239A LYS 3.6 4.0 - - - +
2240A VAL* 4.3 7.4 - - + +
2330A ILE* 4.3 4.7 - - + +
2331A LYS* 1.3 72.2 - - - +
2333A LYS* 1.3 62.6 + - - +
2334A LEU* 4.0 2.8 + - + +
2348A VAL 3.9 0.3 - - - +
2349A ALA* 3.3 22.2 - - - -
2350A THR* 3.2 13.5 + - + +
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Residues in contact with LYS2333 (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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2238A ILE* 3.7 5.5 - - - +
2239A LYS* 2.5 72.2 + - + +
2241A SER* 6.2 0.9 - - - -
2331A LYS* 3.5 21.2 + - - +
2332A VAL* 1.3 72.7 - - - +
2334A LEU* 1.3 68.1 + - - +
2335A THR* 4.3 7.7 + - - +
2347A GLU* 3.4 47.1 + - + -
2348A VAL 3.6 8.1 - - - +
2349A ALA* 4.0 9.6 - - + -
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Residues in contact with LEU2334 (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* 5.6 2.7 - - - +
2204A LEU* 4.6 21.1 - - + -
2206A LEU* 3.4 35.7 - - + -
2227A VAL* 4.3 12.6 - - + -
2235A VAL* 4.2 11.9 - - + -
2237A LYS 4.0 0.4 - - - -
2238A ILE* 3.8 37.0 - - + -
2332A VAL* 4.9 3.8 - - + +
2333A LYS* 1.3 75.5 - - - +
2335A THR* 1.3 62.2 + - - +
2336A VAL* 3.9 9.9 - - + -
2346A SER 3.8 1.0 - - - +
2347A GLU* 3.4 8.5 - - - +
2348A VAL* 2.6 53.3 + - + +
2349A ALA* 6.2 0.2 - - - -
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Residues in contact with THR2335 (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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2235A VAL* 3.6 3.0 - - - +
2236A LYS* 2.8 37.5 + - + +
2237A LYS* 3.1 41.3 + - + +
2239A LYS* 5.8 3.5 + - - +
2333A LYS* 4.8 12.6 + - - +
2334A LEU* 1.3 73.3 + - - +
2336A VAL* 1.3 63.2 + - - +
2345A SER* 4.5 18.6 - - - +
2346A SER 4.4 1.3 - - - -
2347A GLU* 4.9 10.3 + - + +
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Residues in contact with VAL2336 (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* 4.9 13.0 - - + -
2204A LEU* 4.9 13.2 - - + -
2231A THR* 6.1 2.2 - - + -
2233A LYS* 3.9 17.3 - - + -
2234A VAL 3.5 16.2 - - - +
2235A VAL* 4.2 17.9 - - + -
2236A LYS* 5.3 1.3 - - - -
2334A LEU* 4.5 13.0 - - + -
2335A THR* 1.3 77.5 - - - +
2337A SER* 1.3 74.1 + - - +
2345A SER* 3.2 9.3 - - - -
2346A SER* 3.0 45.2 + - - +
2348A VAL* 4.9 8.7 - - + -
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Residues in contact with SER2337 (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* 6.0 1.2 - - - -
2233A LYS* 3.9 15.8 - - - +
2234A VAL* 3.2 32.4 + - - +
2236A LYS* 4.7 13.3 - - - +
2335A THR 4.4 0.4 + - - -
2336A VAL* 1.3 84.0 - - - +
2338A GLY* 1.3 67.6 + - - +
2339A PHE 3.8 0.5 + - - -
2342A GLU* 4.9 18.2 + - - +
2344A THR 4.1 3.1 - - - -
2345A SER* 4.7 1.1 - - - +
2346A SER* 4.8 1.0 - - - -
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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