Contacts of the strand formed by residues 150 - 158 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE 5.3 0.9 - - - +
146A ILE* 3.8 24.4 + - + +
147A ASP 3.6 17.0 - - - -
148A GLY* 2.9 10.6 + - - +
149A ASP* 1.3 89.3 - - + +
151A PHE* 1.3 60.9 + - - +
152A SER 3.9 0.7 + - - -
492A THR* 4.1 9.4 - - + -
493A VAL 3.2 8.5 - - - +
494A LYS* 3.7 23.8 - - + -
495A VAL* 3.7 7.3 - - - +
498A LYS* 4.5 10.3 - - - +
3101A GAI 3.7 19.1 - - - -
455B CYS* 3.8 17.3 - - + -
458B VAL* 3.7 38.1 - - + -
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Residues in contact with PHE 151 (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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143A THR* 4.1 16.6 - - + -
150A PHE* 1.3 72.5 - - - +
152A SER* 1.3 64.2 + - - +
153A TYR* 3.5 39.0 - + + -
491A VAL 3.7 1.7 - - - +
492A THR* 3.4 1.3 - - - -
493A VAL* 2.7 46.2 + - + +
495A VAL* 3.8 17.1 - - + +
3116A EDO 3.2 36.6 - - - -
440C ASN* 4.6 9.2 - - - -
151D PHE* 4.2 3.4 - + - -
153D TYR* 3.4 50.7 - + - -
155D ARG* 5.1 0.9 - - + -
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Residues in contact with SER 152 (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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143A THR* 3.5 3.3 - - - -
144A ILE* 2.8 44.3 + - - +
146A ILE* 4.1 14.1 - - - -
150A PHE 3.9 2.4 + - - -
151A PHE* 1.3 78.2 - - - +
153A TYR* 1.3 64.6 + - - +
490A THR* 3.8 5.4 - - - +
491A VAL 3.3 3.8 + - - -
492A THR* 3.0 20.9 + - - -
463B SER* 2.7 27.6 + - - -
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Residues in contact with TYR 153 (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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142A LYS 3.1 14.1 - - - +
143A THR* 4.1 9.2 - - + +
144A ILE* 4.5 1.6 - - - +
151A PHE* 3.5 36.3 - + + -
152A SER* 1.3 76.6 + - - +
154A THR* 1.3 70.6 + - - +
155A ARG* 3.8 22.7 - - + -
490A THR* 3.4 4.1 - - - +
491A VAL* 2.8 68.3 + - + +
493A VAL* 4.4 5.5 - - + +
3109A EDO 2.6 28.2 + - - -
440B ASN* 4.4 4.9 + - - -
443B SER* 3.9 2.1 + - - -
143D THR* 3.9 14.4 - - + -
151D PHE* 3.4 27.9 - + - -
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Residues in contact with THR 154 (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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141A GLY* 3.4 3.7 - - - -
142A LYS* 2.8 26.5 + - - +
144A ILE* 3.8 14.1 - - + -
153A TYR* 1.3 79.2 - - - +
155A ARG* 1.3 63.2 + - - +
488A VAL* 3.9 10.1 - - + -
489A LYS 3.1 6.1 - - - -
490A THR* 3.6 22.4 - - - +
464B PRO* 3.7 20.2 - - + -
480B TYR* 2.6 25.6 + - - +
143D THR* 2.9 28.4 + - - +
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Residues in contact with ARG 155 (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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153A TYR* 3.8 13.2 - - + -
154A THR* 1.3 77.7 - - - +
156A HIS* 1.3 62.9 + - - +
157A GLU* 3.0 39.1 + - + +
487A LYS 3.5 3.1 - - - +
488A VAL* 3.6 2.8 - - - +
489A LYS* 2.9 38.9 + - + +
491A VAL* 4.5 7.6 - - - -
3109A EDO 2.8 54.4 + - - +
444B GLN* 3.5 37.4 + - - +
143D THR* 4.5 9.0 - - - +
151D PHE* 5.3 0.4 - - + -
498D LYS* 6.3 0.6 - - - +
499D ASN 4.0 10.9 + - - -
500D SER* 4.5 4.3 + - - -
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Residues in contact with HIS 156 (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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139A TYR* 3.1 55.1 - + + +
140A HIS 3.2 26.2 + - - -
141A GLY* 3.9 9.1 - - - +
142A LYS* 5.6 2.7 - - - -
154A THR* 4.4 2.0 - - - -
155A ARG* 1.3 79.1 - - - +
157A GLU* 1.3 62.1 + - - +
158A PRO* 4.8 0.2 - - - +
185A THR 5.5 1.2 - - - +
486A THR* 4.2 11.3 - - - +
487A LYS 3.5 4.9 - - - -
488A VAL* 4.1 14.6 - - + -
480B TYR* 3.0 38.0 + + - -
500D SER* 4.3 5.1 - - - +
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Residues in contact with GLU 157 (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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77A ARG* 5.5 4.4 + - - +
155A ARG* 3.0 39.1 + - + +
156A HIS* 1.3 74.7 - - - +
158A PRO* 1.3 72.7 - - + +
185A THR 5.0 0.4 - - - -
486A THR* 3.1 7.9 - - - -
487A LYS* 2.7 52.1 + - + +
489A LYS* 3.0 42.3 + - - +
444B GLN 4.2 1.1 - - - +
447B GLN* 6.1 0.9 - - - -
500D SER* 3.7 16.4 - - - +
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Residues in contact with PRO 158 (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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70A PHE* 3.6 21.6 - - + -
77A ARG* 4.6 1.8 - - - +
156A HIS 4.8 0.2 - - - +
157A GLU* 1.3 92.9 - - + +
159A VAL* 1.3 64.7 + - - +
185A THR 3.3 25.1 - - - +
186A GLY 3.6 17.3 - - - +
187A ASN* 3.5 11.2 - - - +
485A TYR 3.8 6.1 - - - +
486A THR* 4.5 0.4 - - + -
487A LYS* 3.9 11.1 - - - +
500D SER* 3.5 37.0 - - - +
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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