Contacts of the strand formed by residues 321 - 332 (chain 3) in PDB entry 5Z58
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 MET 321 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2633 ASP* 3.2 42.0 - - - +
2643 GLN* 3.5 14.8 - - - +
2653 PRO* 5.9 2.0 - - - -
3173 THR* 3.3 2.0 - - - -
3183 ASP* 2.3 55.5 + - + +
3193 GLU* 3.3 2.9 - - - +
3203 ASP* 1.3 93.4 - - - +
3223 VAL* 1.3 59.0 + - - +
3233 THR* 3.4 3.9 + - + +
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Residues in contact with VAL 322 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2453 PRO* 5.0 9.4 - - + -
2583 TYR* 3.4 27.8 - - + -
2643 GLN* 3.0 35.1 - - - +
2653 PRO* 5.4 1.6 - - - +
2673 ILE* 3.2 17.3 - - + +
3153 LEU* 4.6 16.4 - - + -
3163 GLU 3.1 24.5 - - - +
3173 THR* 3.7 8.0 + - - +
3203 ASP 3.7 2.0 + - - -
3213 MET* 1.3 70.8 - - - +
3233 THR* 1.3 58.2 + - - +
3243 GLU 3.3 16.4 - - - +
3253 ILE* 4.7 2.2 - - + -
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Residues in contact with THR 323 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2673 ILE* 3.4 11.9 - - - +
3163 GLU* 2.9 14.3 + - - +
3173 THR 4.7 1.4 + - - -
3183 ASP* 4.0 26.2 - - + +
3213 MET* 3.4 3.8 + - + +
3223 VAL* 1.3 75.2 - - - +
3243 GLU* 1.3 73.6 + - - +
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Residues in contact with GLU 324 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2673 ILE* 3.6 6.4 - - - +
3163 GLU* 3.1 50.2 + - + +
3223 VAL* 3.3 8.1 - - - +
3233 THR* 1.3 85.3 + - - +
3253 ILE* 1.3 65.4 + - - +
3263 ARG* 5.2 2.7 - - - -
3743 SER* 3.0 22.2 + - - +
3753 SER* 3.2 12.1 - - - +
3763 ALA* 3.2 22.1 - - + +
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Residues in contact with ILE 325 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2493 LEU* 4.8 4.3 - - + -
2563 ILE* 5.3 9.2 - - + +
2583 TYR* 3.6 30.1 - - + +
2673 ILE* 3.6 31.0 - - + +
2683 ARG 5.7 0.9 - - - -
2693 CYS* 5.2 4.7 - - + -
3133 ILE* 4.6 5.2 - - + -
3143 THR 3.3 15.0 - - - +
3153 LEU* 4.4 14.1 - - + -
3163 GLU 4.7 0.9 - - - +
3223 VAL* 4.7 0.7 - - + -
3243 GLU* 1.3 80.8 - - - +
3263 ARG* 1.3 62.9 + - - +
3273 LEU* 3.4 25.0 + - + +
3743 SER* 3.1 1.9 + - - -
3753 SER* 2.3 53.8 + - - +
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Residues in contact with ARG 326 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3123 LYS 3.8 0.5 - - - +
3143 THR* 3.0 44.7 + - - +
3163 GLU* 3.0 43.2 + - + +
3243 GLU* 5.2 3.4 - - + -
3253 ILE* 1.3 79.5 - - - +
3273 LEU* 1.3 62.9 + - - +
3283 LYS 4.1 0.4 + - - -
3723 GLU* 2.8 47.0 + - + +
3733 PHE 3.0 13.9 + - - +
3743 SER* 4.0 13.2 - - - +
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Residues in contact with LEU 327 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2563 ILE* 4.3 22.2 - - + -
2693 CYS* 5.3 9.2 - - - -
2703 PRO 5.2 2.7 - - - +
2713 ILE* 6.0 0.4 - - - -
2723 PRO* 4.8 15.3 - - + -
2873 PHE* 4.9 6.3 - - + -
3113 PHE* 4.4 25.1 - - + -
3123 LYS 3.7 3.6 - - - +
3133 ILE* 3.8 35.4 - - + -
3253 ILE* 3.4 31.1 + - + -
3263 ARG* 1.3 75.4 - - - +
3283 LYS* 1.3 59.5 + - - +
3723 GLU* 5.0 0.2 - - - -
3733 PHE* 2.9 47.3 + - + +
3743 SER* 4.8 0.6 - - - +
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Residues in contact with LYS 328 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3113 PHE* 3.7 4.9 - - - -
3123 LYS* 3.2 35.8 + - + +
3263 ARG 4.1 0.8 - - - -
3273 LEU* 1.3 74.0 - - - +
3293 TYR* 1.3 79.7 + - + +
3303 PHE* 3.2 0.7 + - - -
3653 GLY 2.7 23.3 + - - +
3663 ASP* 4.4 15.3 - - - +
3673 ASP 4.8 2.0 - - - +
3683 ASP* 4.0 5.6 + - - -
3703 GLU* 2.5 53.8 + - - +
3713 PRO 3.6 11.0 - - - +
3723 GLU* 3.6 39.2 - - + +
3943 ASN* 4.9 1.2 - - - +
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Residues in contact with TYR 329 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2743 ARG* 5.8 0.4 - - - -
3093 ASP* 4.7 1.6 - - + -
3113 PHE* 3.3 34.1 - + + -
3273 LEU 4.2 0.8 + - - -
3283 LYS* 1.3 95.7 + - - +
3303 PHE* 1.3 67.8 + - - +
3313 ASP* 4.1 10.6 - - - -
3323 THR* 3.0 37.3 + - + +
3703 GLU* 4.3 4.0 - - + +
3713 PRO* 4.2 12.1 + - + +
3733 PHE* 5.6 6.3 - - + -
3873 PHE* 3.3 39.9 - + + -
3883 GLN 4.4 5.8 - - - -
3893 PRO* 4.0 13.8 - - + +
3903 ARG* 3.1 54.1 + - + -
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Residues in contact with PHE 330 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3003 PHE* 5.5 4.9 - + - -
3023 LEU* 4.3 17.3 - - + -
3103 ILE* 3.0 33.1 + - + +
3113 PHE* 3.9 0.4 - - - -
3123 LYS* 3.7 42.0 - - + +
3283 LYS 3.2 1.6 + - - -
3293 TYR* 1.3 75.7 - - - +
3313 ASP* 1.3 85.6 + - + +
3473 LEU* 5.3 4.7 - - + -
3613 ILE* 4.8 15.0 - - + -
3633 HIS 5.3 2.2 - - - -
3643 LEU* 4.3 17.7 - - - -
3653 GLY 5.9 0.7 - - - -
3903 ARG* 4.0 6.1 + - - -
3943 ASN* 2.3 45.8 + - + +
3953 LEU* 4.5 24.0 - - + -
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Residues in contact with ASP 331 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3093 ASP* 3.8 0.5 - - - -
3103 ILE* 2.8 30.3 + - + +
3293 TYR* 4.1 11.4 - - - -
3303 PHE* 1.3 101.0 - - + +
3323 THR* 1.3 69.9 + - - +
3333 VAL* 5.5 0.9 - - + -
3903 ARG* 4.7 4.9 + - - -
3913 PRO 4.4 2.4 - - - +
3923 LEU* 3.6 19.8 - - + +
3933 LYS 3.6 7.8 + - - -
3943 ASN* 3.0 36.6 + - - +
3953 LEU* 3.1 25.9 + - + +
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Residues in contact with THR 332 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3073 GLN 5.5 1.3 - - - -
3083 GLY 3.2 8.5 - - - +
3093 ASP* 3.1 30.5 - - - +
3103 ILE* 4.4 0.7 - - - +
3293 TYR* 3.0 25.4 - - + +
3313 ASP* 1.3 79.9 - - - +
3333 VAL* 1.3 62.9 + - - +
3893 PRO* 5.8 1.1 - - + -
3903 ARG 3.7 17.3 + - - -
3913 PRO 5.4 0.6 + - - -
3923 LEU* 3.2 22.2 - - - +
8513 ILE* 4.9 16.9 + - - +
8523 PHE* 3.8 19.5 - - + -
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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