Contacts of the helix formed by residues 2310 - 2323 (chain A) in PDB entry 5ZCS
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 SER2310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362A GLU* 5.7 2.7 - - - -
1394A ALA* 3.6 24.2 - - - +
1395A LYS* 3.3 38.7 + - - +
1398A HIS* 6.5 0.7 - - - -
2304A TRP* 4.5 20.2 - - - -
2309A SER* 1.3 75.2 - - - +
2311A GLU* 1.3 67.5 + - - +
2312A VAL 3.4 1.6 - - - -
2313A TRP* 3.6 10.5 - - - +
2314A PHE* 3.2 21.1 + - - +
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Residues in contact with GLU2311 (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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1392A ALA* 5.4 3.5 - - - +
1394A ALA* 3.8 17.2 + - + +
1395A LYS* 2.7 35.3 + - - +
2309A SER* 3.6 16.0 + - - +
2310A SER* 1.3 80.2 - - - +
2312A VAL* 1.3 63.9 + - + +
2313A TRP 3.5 0.2 + - - -
2314A PHE* 4.7 1.4 - - - +
2315A ASP* 2.9 29.7 + - - +
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Residues in contact with VAL2312 (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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2307A SER* 5.2 1.1 - - - -
2308A PRO* 5.4 14.8 - - + -
2309A SER* 3.7 17.6 + - - +
2310A SER 3.4 0.2 - - - -
2311A GLU* 1.3 78.7 - - + +
2313A TRP* 1.3 59.1 + - - +
2315A ASP* 3.4 7.2 + - + +
2316A ARG* 2.9 51.6 + - + +
2349A LEU 5.3 2.2 - - - +
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Residues in contact with TRP2313 (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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1394A ALA 5.9 0.2 - - - -
1397A LEU* 4.6 11.7 - - + -
1398A HIS* 4.6 11.2 - + + -
1401A GLU* 6.6 0.2 - - + -
2300A ALA 4.0 17.5 - - - -
2303A LEU* 3.2 40.2 - - + +
2304A TRP* 3.3 39.0 - + + +
2307A SER* 3.3 33.8 - - - +
2309A SER 3.3 11.3 + - - +
2310A SER* 3.6 10.9 - - - +
2311A GLU 3.2 0.8 - - - -
2312A VAL* 1.3 79.6 - - - +
2314A PHE* 1.3 70.0 + - + +
2316A ARG* 3.3 5.1 + - + +
2317A ARG* 2.9 73.5 + - + +
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Residues in contact with PHE2314 (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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1394A ALA* 5.3 3.1 - - + -
1397A LEU* 3.6 40.4 - - + -
1423A LEU* 4.7 18.8 - - + -
1425A GLN* 5.4 8.3 - - + -
1428A ALA* 5.6 10.1 - - + -
2310A SER 3.2 13.8 + - - +
2311A GLU 4.8 1.8 - - - +
2313A TRP* 1.3 81.7 - - + +
2315A ASP* 1.3 67.8 + - - +
2317A ARG* 3.4 34.3 - - - -
2318A THR* 2.6 60.1 + - + -
2322A ARG* 6.1 0.2 - - - -
2388A GLU* 5.1 13.7 - - + -
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Residues in contact with ASP2315 (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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1425A GLN* 5.8 1.6 + - - -
2311A GLU* 2.9 18.3 + - - +
2312A VAL* 3.4 12.1 + - + +
2313A TRP 3.3 0.4 - - - -
2314A PHE* 1.3 87.3 - - - +
2316A ARG* 1.3 57.3 + - + +
2318A THR* 3.8 2.6 - - - -
2319A ASN* 2.8 41.7 + - - +
2322A ARG* 3.8 7.1 + - - +
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Residues in contact with ARG2316 (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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2303A LEU* 5.2 18.7 - - + +
2306A LYS* 3.5 28.0 + - - +
2307A SER* 4.8 15.2 - - - +
2308A PRO* 5.5 2.6 - - - +
2312A VAL* 2.9 39.2 + - + +
2313A TRP* 3.9 5.8 - - + +
2315A ASP* 1.3 74.2 - - + +
2317A ARG* 1.3 61.5 + - - +
2319A ASN* 3.3 3.4 + - - +
2320A TYR* 2.9 26.9 + - - +
2346A LEU* 5.5 2.4 - - - +
2347A ASP 4.0 4.4 + - - -
2348A ARG* 3.1 34.8 + - - +
2349A LEU* 3.5 25.2 + - - +
2350A SER* 3.4 28.1 - - - +
2351A GLY* 4.4 5.1 - - - +
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Residues in contact with ARG2317 (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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1397A LEU* 4.1 13.9 + - - +
1401A GLU* 5.6 8.5 - - - +
2300A ALA* 5.3 16.4 - - - +
2303A LEU* 5.2 17.6 - - + +
2313A TRP* 2.9 59.9 + - + +
2314A PHE* 3.4 36.3 - - - +
2316A ARG* 1.3 76.3 - - - +
2318A THR* 1.3 61.4 + - - +
2320A TYR* 3.4 21.2 + - + +
2321A THR* 3.5 10.2 + - - -
2386A ALA 4.4 17.3 + - - +
2388A GLU* 4.4 21.0 - - - +
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Residues in contact with THR2318 (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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1427A GLU* 5.6 2.0 - - + +
2314A PHE* 2.6 54.7 + - + -
2315A ASP* 4.0 1.3 - - - -
2317A ARG* 1.3 75.0 + - - +
2319A ASN* 1.3 61.1 + - - +
2320A TYR 3.2 0.4 - - - -
2321A THR* 3.2 3.5 + - - +
2322A ARG* 2.9 55.9 + - - +
2395A ASN* 3.3 19.6 + - + +
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Residues in contact with ASN2319 (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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2315A ASP* 2.8 35.3 + - - +
2316A ARG* 3.3 5.2 + - - +
2318A THR* 1.3 73.6 - - - +
2320A TYR* 1.3 58.3 + - - +
2321A THR 3.4 0.2 + - - -
2322A ARG* 2.5 34.2 + - - +
2323A SER* 2.6 34.7 + - - -
2350A SER* 3.7 14.1 + - - +
2351A GLY 3.0 18.3 - - - +
2352A LYS* 4.2 19.8 + - + +
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Residues in contact with TYR2320 (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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2246A LEU* 4.2 23.2 - - + +
2299A LEU* 5.0 8.7 - - + +
2303A LEU* 6.1 12.6 - - + -
2316A ARG 2.9 13.1 + - - +
2317A ARG* 3.4 16.4 - - + +
2318A THR 3.2 0.2 - - - -
2319A ASN* 1.3 78.9 - - - +
2321A THR* 1.3 62.6 + - - +
2323A SER* 4.2 1.1 + - - -
2324A LEU* 3.3 16.8 - - + +
2344A LEU* 5.0 6.2 - - + +
2346A LEU* 3.6 29.6 - - + -
2351A GLY* 3.6 5.8 + - - +
2353A ILE* 3.7 30.4 - - + +
2383A LEU* 4.1 26.8 - - + +
2386A ALA* 3.7 31.2 - - + -
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Residues in contact with THR2321 (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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2317A ARG 3.5 11.3 + - - -
2318A THR* 3.2 4.7 + - - -
2320A TYR* 1.3 82.5 - - - +
2322A ARG* 1.3 64.1 + - - +
2323A SER 3.2 3.6 + - - -
2324A LEU* 3.3 28.4 + - + +
2325A ALA* 4.1 3.6 + - - +
2386A ALA* 4.2 13.3 + - - +
2387A MET* 4.1 25.6 + - + -
2395A ASN* 3.5 38.2 - - + +
2396A TYR* 6.2 0.7 - - + -
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Residues in contact with ARG2322 (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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1425A GLN* 3.8 23.6 + - - +
1427A GLU* 4.1 3.8 + - - -
2218A LYS* 3.3 38.6 + - - +
2220A LEU* 5.2 2.3 - - - +
2314A PHE* 6.1 0.4 - - - -
2315A ASP* 3.8 8.9 + - - +
2318A THR* 2.9 41.1 + - - +
2319A ASN* 2.5 59.0 + - - +
2321A THR* 1.3 75.5 - - - +
2323A SER* 1.3 61.9 + - - +
2324A LEU 3.5 0.7 - - - -
2325A ALA 4.5 0.4 + - - -
2326A VAL* 3.9 9.5 - - - +
2395A ASN* 3.2 24.9 - - - +
2399A THR* 3.6 20.8 - - - +
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Residues in contact with SER2323 (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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2220A LEU* 5.9 2.5 - - - -
2222A ILE* 5.4 7.4 - - - +
2319A ASN 2.6 23.8 + - - -
2321A THR 3.2 0.4 - - - -
2322A ARG* 1.3 81.0 - - - +
2324A LEU* 1.3 58.4 + - - +
2325A ALA 3.6 0.9 - - - -
2326A VAL* 3.4 14.1 - - - +
2327A MET* 3.4 22.3 - - - +
2351A GLY 4.0 0.9 + - - -
2352A LYS* 4.7 12.3 - - - -
2353A ILE* 3.3 35.2 + - - +
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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