Contacts of the strand formed by residues 150 - 158 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455K CYS* 3.9 14.8 - - + -
458K VAL* 3.6 43.7 - - + -
144L ILE 5.4 1.0 - - - +
146L ILE* 3.5 25.1 + - + +
147L ASP 3.5 20.6 - - - -
148L GLY* 2.9 13.5 + - - +
149L ASP* 1.3 88.5 - - - +
151L PHE* 1.3 60.1 + - - +
152L SER 4.0 1.1 + - - -
492L THR* 4.1 6.5 - - + -
493L VAL 3.2 9.4 - - - +
494L LYS* 3.7 20.6 - - + -
495L VAL* 3.8 9.3 - - - +
498L LYS* 4.3 13.9 - - - +
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Residues in contact with PHE 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I PHE* 4.4 2.5 - + - -
153I TYR* 3.4 53.4 - + - -
155I ARG* 5.0 7.2 - - + -
440J ASN* 4.5 14.6 - - - -
444J GLN* 5.5 1.1 - - - +
143L THR* 4.1 18.8 - - + -
150L PHE* 1.3 73.0 - - - +
152L SER* 1.3 64.3 + - - +
153L TYR* 3.6 35.9 - + + -
491L VAL 3.6 1.7 - - - +
492L THR* 3.4 1.3 - - - -
493L VAL* 2.7 47.9 + - + +
495L VAL* 3.8 20.0 - - + -
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Residues in contact with SER 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463K SER* 2.8 26.9 + - - -
143L THR* 3.5 4.2 - - - -
144L ILE* 2.8 41.6 + - - +
146L ILE* 3.8 16.8 - - - -
150L PHE 4.0 1.8 + - - -
151L PHE* 1.3 77.9 - - - +
153L TYR* 1.3 65.7 + - - +
490L THR* 3.5 6.1 - - - +
491L VAL 3.2 3.6 - - - -
492L THR* 2.9 21.2 + - - -
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Residues in contact with TYR 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I THR* 3.9 10.8 - - + -
151I PHE* 3.4 32.1 - + - -
440K ASN* 4.5 4.5 + - - -
443K SER* 3.9 1.4 + - - -
142L LYS 3.0 13.9 - - - +
143L THR* 4.1 9.4 - - + +
144L ILE* 4.5 1.8 - - - +
151L PHE* 3.6 32.5 - + + -
152L SER* 1.3 76.4 + - - +
154L THR* 1.3 76.3 + - - +
155L ARG* 3.7 15.9 - - - -
490L THR* 3.3 4.7 - - - +
491L VAL* 2.8 66.1 + - + +
493L VAL* 4.5 5.6 - - + +
3129L EDO 2.5 34.3 + - - -
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Residues in contact with THR 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I THR* 3.0 26.5 + - - +
464K PRO* 3.9 20.4 - - + -
480K TYR* 2.7 29.0 + - - +
141L GLY* 3.5 3.6 - - - -
142L LYS* 2.7 31.9 + - - -
144L ILE* 4.0 9.9 - - + -
153L TYR* 1.3 78.8 - - - +
155L ARG* 1.3 64.2 + - - +
156L HIS* 4.7 0.9 - - - -
488L VAL* 4.1 8.3 - - + -
489L LYS 3.1 5.2 - - - +
490L THR* 3.5 24.5 - - - +
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Residues in contact with ARG 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I THR* 4.6 8.5 - - - +
151I PHE* 5.3 1.8 - - + -
498I LYS* 6.3 0.2 - - - +
499I ASN 4.4 8.1 + - - -
500I SER* 5.1 4.6 + - - -
444K GLN* 3.4 40.6 + - - +
153L TYR* 3.7 21.1 - - + -
154L THR* 1.3 76.9 - - - +
156L HIS* 1.3 63.5 + - - +
157L GLU* 2.7 38.4 + - + +
487L LYS 3.4 4.0 - - - +
488L VAL* 3.6 1.7 - - - -
489L LYS* 2.8 52.2 + - + +
491L VAL* 4.7 2.7 - - - -
3129L EDO 2.8 36.2 + - - +
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Residues in contact with HIS 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500I SER* 4.2 6.3 - - - +
480K TYR* 2.9 41.3 + + - -
483K GLN* 6.2 0.4 - - - -
139L TYR* 3.2 49.9 - + + +
140L HIS 3.3 23.3 + - - -
141L GLY* 3.9 11.4 - - - +
142L LYS* 5.6 3.4 - - - -
154L THR* 4.4 2.0 - - - -
155L ARG* 1.3 78.9 - - - +
157L GLU* 1.3 61.8 + - - +
158L PRO* 4.7 0.5 - - - +
185L THR 5.6 0.9 - - - +
486L THR* 3.3 16.6 + - + +
487L LYS 3.5 4.7 - - - -
488L VAL* 4.0 13.2 - - + -
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Residues in contact with GLU 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500I SER* 3.8 15.7 - - - +
444K GLN 5.3 0.9 - - - -
447K GLN* 6.0 0.9 - - - -
77L ARG* 5.3 4.9 + - - +
155L ARG* 2.7 44.2 + - + +
156L HIS* 1.3 75.6 - - - +
158L PRO* 1.3 73.4 - - + +
185L THR 4.9 0.7 - - - -
486L THR* 3.3 6.5 - - - -
487L LYS* 2.6 48.7 + - + +
489L LYS* 2.9 35.4 + - + +
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Residues in contact with PRO 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500I SER* 3.5 34.3 - - - +
70L PHE* 3.5 22.6 - - + -
77L ARG* 5.0 1.1 - - - +
156L HIS 4.7 0.4 - - - +
157L GLU* 1.3 94.7 - - + +
159L VAL* 1.3 64.6 + - - +
185L THR 3.1 24.5 - - - +
186L GLY 3.5 22.7 - - - +
187L ASN* 3.6 7.6 - - - +
485L TYR 3.8 7.0 - - - +
486L THR* 5.4 0.2 - - - +
487L LYS* 3.9 10.6 - - - +
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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