Contacts of the strand formed by residues 150 - 158 (chain D) in PDB entry 1ZUM
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 PHE 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C TRP* 6.3 1.1 - + - -
455C CYS* 3.8 22.9 - - + -
458C VAL* 3.6 41.7 - - + -
144D ILE 5.5 0.5 - - - +
146D ILE* 3.9 20.8 - - + +
147D ASP 3.4 18.6 - - - -
148D GLY* 3.0 16.2 + - - +
149D ASP* 1.3 91.2 - - + +
151D PHE* 1.3 59.5 + - - +
152D SER 4.0 0.6 + - - -
492D THR* 4.1 9.0 - - + -
493D VAL 3.1 8.7 - - - +
494D LYS* 3.7 20.9 - - + -
495D VAL* 3.8 7.9 - - - +
498D LYS* 4.4 12.1 - - - +
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Residues in contact with PHE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 4.2 3.1 - + - -
153A TYR* 3.4 48.0 - + - -
155A ARG* 5.3 1.1 - - + -
3109A EDO 3.4 28.5 - - - -
440B ASN* 4.8 8.7 - - - -
143D THR* 4.1 16.2 - - + -
144D ILE 5.8 0.4 - - - -
150D PHE* 1.3 72.7 - - - +
152D SER* 1.3 68.9 + - - +
153D TYR* 3.5 37.0 - + + -
491D VAL 3.7 1.4 - - - +
492D THR* 3.4 0.7 - - - -
493D VAL* 2.8 40.9 + - + +
495D VAL* 3.7 19.3 - - + +
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C SER* 2.7 27.7 + - - -
143D THR* 3.5 1.9 - - - -
144D ILE* 2.7 46.8 + - - +
146D ILE* 4.1 14.8 - - - +
150D PHE 4.0 0.8 - - - -
151D PHE* 1.3 79.7 - - - +
153D TYR* 1.3 60.1 + - - +
490D THR* 3.7 5.4 - - - +
491D VAL 3.1 5.0 + - - -
492D THR* 2.8 22.6 + - - -
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Residues in contact with TYR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.8 15.3 - - + -
151A PHE* 3.4 33.9 - + - -
3116A EDO 2.6 35.7 + - - -
440C ASN* 4.5 4.2 + - - -
443C SER* 4.0 1.9 + - - -
142D LYS 3.0 14.8 - - - +
143D THR* 4.0 9.2 - - + -
144D ILE* 4.4 2.0 - - - +
151D PHE* 3.5 30.5 - + + -
152D SER* 1.3 77.0 + - - +
154D THR* 1.3 70.8 + - - +
155D ARG* 4.0 5.4 - - - -
490D THR* 3.3 5.2 - - - +
491D VAL* 2.8 71.2 + - + +
493D VAL* 4.5 7.0 - - + +
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Residues in contact with THR 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 2.9 28.2 + - - +
464C PRO* 3.8 23.8 - - + -
480C TYR* 2.8 25.1 + - - +
141D GLY* 3.5 2.7 - - - -
142D LYS* 2.8 28.9 + - - +
144D ILE* 4.0 10.1 - - + -
153D TYR* 1.3 79.5 - - - +
155D ARG* 1.3 61.7 + - - +
488D VAL* 3.8 9.2 - - + -
489D LYS 3.0 6.7 - - - -
490D THR* 3.6 23.3 - - + +
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Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 4.5 9.9 - - - +
151A PHE* 5.4 0.7 - - + -
499A ASN 4.3 15.4 + - - -
500A SER* 4.6 8.7 + - - -
3116A EDO 2.7 36.6 + - - +
444C GLN* 3.7 21.8 + - - +
141D GLY* 4.8 0.4 - - - -
153D TYR* 4.0 16.6 - - + -
154D THR* 1.3 78.0 - - - +
156D HIS* 1.3 64.5 + - - +
157D GLU* 2.6 30.3 + - + +
487D LYS 3.6 0.5 - - - +
488D VAL* 3.5 2.9 - - - -
489D LYS* 2.8 59.9 + - + +
491D VAL* 4.9 1.3 - - - +
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Residues in contact with HIS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A SER* 4.1 6.8 - - - +
480C TYR* 3.0 36.1 + + - -
139D TYR* 3.3 48.9 + + + +
140D HIS 3.0 28.2 + - - -
141D GLY* 4.2 7.3 - - - +
142D LYS* 5.9 1.8 - - - -
154D THR* 4.7 0.2 - - - -
155D ARG* 1.3 76.7 - - - +
157D GLU* 1.3 59.4 + - - +
158D PRO* 4.7 0.5 - - - +
185D THR 5.8 0.2 - - - +
486D THR* 3.4 16.5 + - + +
487D LYS 3.5 4.3 - - - -
488D VAL* 3.9 19.0 - - + +
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A SER* 3.7 14.6 - - - +
444C GLN 4.5 0.7 - - - +
447C GLN* 5.9 1.9 - - - -
77D ARG* 5.7 3.2 + - - +
155D ARG* 2.6 45.6 + - - +
156D HIS* 1.3 75.8 - - - +
158D PRO* 1.3 73.8 - - + +
185D THR 4.9 0.9 - - - -
486D THR* 3.2 7.2 - - - -
487D LYS* 2.7 57.3 + - + +
489D LYS* 3.3 29.5 + - + +
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Residues in contact with PRO 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A SER* 3.4 33.2 - - - +
70D PHE* 3.7 21.0 - - + -
77D ARG* 4.8 1.1 - - - +
156D HIS 4.7 0.7 - - - +
157D GLU* 1.3 94.1 - - + +
159D VAL* 1.3 63.2 + - - +
185D THR 3.1 25.8 - - - +
186D GLY 3.6 20.4 - - - +
187D ASN* 3.6 11.7 - - - +
485D TYR 3.8 6.7 - - - +
486D THR* 5.0 0.2 - - - +
487D LYS* 3.6 14.3 + - - -
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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