Contacts of the strand formed by residues 150 - 158 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I ILE 5.3 1.2 - - - +
146I ILE* 4.1 17.2 - - + +
147I ASP 3.6 15.5 - - - -
148I GLY* 3.0 10.9 + - - +
149I ASP* 1.3 88.5 - - + +
151I PHE* 1.3 61.1 + - - +
152I SER 3.9 1.3 + - - -
492I THR* 4.1 13.5 - - + -
493I VAL 3.1 8.7 - - - +
494I LYS* 3.5 26.2 - - + -
495I VAL* 3.9 6.8 - - - +
498I LYS* 4.3 12.3 - - - +
3107I GAI 3.6 20.0 - - - -
455J CYS* 3.9 16.6 - - + -
458J VAL* 3.7 39.5 - - + -
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Residues in contact with PHE 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I THR* 4.2 16.2 - - + -
150I PHE* 1.3 72.2 - - - +
152I SER* 1.3 64.8 + - - +
153I TYR* 3.6 35.6 - + + -
491I VAL 3.6 2.3 - - - +
492I THR* 3.5 1.1 - - - -
493I VAL* 2.8 46.4 + - + +
495I VAL* 3.8 19.0 - - + +
440K ASN* 4.8 9.6 - - - -
151L PHE* 4.4 2.5 - + - -
153L TYR* 3.4 56.5 - + - -
155L ARG* 5.1 2.7 - - + -
3129L EDO 3.8 23.6 - - - -
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Residues in contact with SER 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I THR* 3.5 3.5 - - - -
144I ILE* 2.7 43.0 + - - +
146I ILE* 3.8 19.5 - - - -
150I PHE 3.9 1.2 - - - -
151I PHE* 1.3 78.9 - - - +
153I TYR* 1.3 61.1 + - - +
490I THR* 3.7 4.9 - - - +
491I VAL 3.3 3.7 + - - -
492I THR* 3.0 21.0 + - - -
463J SER* 2.7 28.0 + - - -
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Residues in contact with TYR 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I LYS 3.1 13.5 - - - +
143I THR* 4.1 9.0 - - + -
144I ILE* 4.5 2.2 - - - +
151I PHE* 3.6 33.0 - + + -
152I SER* 1.3 76.7 + - - +
154I THR* 1.3 68.3 + - - +
155I ARG* 3.7 23.5 - - - -
490I THR* 3.4 4.4 - - - +
491I VAL* 2.8 71.9 + - + +
493I VAL* 4.5 5.7 - - + +
440J ASN* 4.5 6.2 + - - -
443J SER* 4.1 10.4 + - - -
143L THR* 3.9 15.5 - - + -
151L PHE* 3.4 36.8 - + - -
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Residues in contact with THR 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I GLY* 3.5 3.4 - - - -
142I LYS* 2.7 31.4 + - - -
144I ILE* 3.9 7.2 - - + -
153I TYR* 1.3 76.2 - - - +
155I ARG* 1.3 64.3 + - - +
488I VAL* 4.0 8.3 - - + -
489I LYS 3.1 5.6 - - - -
490I THR* 3.5 23.3 - - - +
464J PRO* 3.6 24.7 - - + -
480J TYR* 2.7 29.3 + - + -
143L THR* 2.9 28.2 + - - +
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Residues in contact with ARG 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I TYR* 3.7 29.6 + - + -
154I THR* 1.3 75.4 - - - +
156I HIS* 1.3 64.7 + - - +
157I GLU* 2.7 34.5 + - + +
487I LYS 3.4 3.1 - - - +
488I VAL* 3.6 2.1 - - - -
489I LYS* 2.8 49.5 + - + +
491I VAL* 4.7 4.7 - - - +
443J SER 5.0 0.8 + - - -
444J GLN* 3.7 39.3 + - - +
143L THR* 4.5 10.3 - - - +
151L PHE* 5.0 7.2 - - + -
499L ASN 4.5 13.9 + - - -
500L SER* 5.1 4.2 + - - -
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Residues in contact with HIS 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I TYR* 3.3 52.9 - + + +
140I HIS 3.0 29.0 + - - -
141I GLY* 4.0 7.9 - - - +
142I LYS* 5.7 3.4 - - + -
154I THR* 4.6 0.4 - - - -
155I ARG* 1.3 76.3 - - - +
157I GLU* 1.3 63.0 + - - +
158I PRO* 4.6 0.9 - - - +
185I THR 5.5 1.0 - - - +
486I THR* 4.2 10.3 - - + +
487I LYS 3.5 3.8 - - - -
488I VAL* 4.0 18.2 - - + -
480J TYR* 3.0 37.3 + + - -
500L SER* 4.3 5.4 - - - +
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Residues in contact with GLU 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ARG* 5.4 5.1 + - - +
155I ARG* 2.7 46.2 + - + +
156I HIS* 1.3 76.1 - - - +
158I PRO* 1.3 75.5 - - + +
185I THR 4.9 0.2 - - - -
486I THR* 3.1 7.7 - - - -
487I LYS* 2.6 41.4 + - + +
489I LYS* 3.3 16.1 + - - -
444J GLN 4.4 1.2 - - - +
468J TYR* 2.8 36.3 + - - +
500L SER* 3.8 13.9 - - - +
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Residues in contact with PRO 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I PHE* 3.6 24.6 - - + -
77I ARG* 4.6 4.9 - - - +
156I HIS 4.6 0.7 - - - +
157I GLU* 1.3 92.3 - - + +
159I VAL* 1.3 64.8 + - - +
185I THR 3.1 24.7 - - - +
186I GLY* 3.7 14.1 - - - +
187I ASN* 3.5 11.4 - - - +
485I TYR 3.8 7.2 - - - +
486I THR* 4.9 0.2 - - + -
487I LYS* 3.8 10.6 - - - +
500L SER* 3.3 35.7 - - - +
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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