Contacts of the strand formed by residues 44 - 51 (chain B) in PDB entry 1NTZ
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 ALA 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ASN* 5.0 4.9 - - - +
366A VAL* 3.8 20.1 - - + +
367A SER* 5.7 3.1 - - - +
40B ASN* 4.8 0.5 + - - -
42B ALA* 3.2 23.2 - - + +
43B PRO* 1.3 79.5 - - - +
45B SER* 1.3 67.0 + - - +
46B ARG* 6.1 2.9 - - - +
110B GLU* 6.1 3.1 - - + -
111B CYS 3.4 15.7 - - - +
112B LEU* 3.8 6.1 - - + +
113B ARG 4.3 0.9 - - - -
209B LEU 4.3 2.8 - - - +
210B GLY* 4.4 2.9 - - - -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 1.3 78.2 + - - +
46B ARG* 1.3 64.0 + - - +
47B ILE* 4.3 2.2 - - - -
109B VAL 4.7 0.2 - - - -
110B GLU* 3.5 8.0 - - - +
111B CYS* 2.5 36.9 + - - -
113B ARG* 3.7 11.1 - - - +
116B VAL* 3.4 30.7 - - - +
209B LEU 3.2 8.7 - - - -
210B GLY 2.9 23.8 + - - -
211B VAL* 4.7 2.0 - - - -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A SER* 4.8 8.9 + - - +
370A ASP* 4.4 4.9 + - - -
45B SER* 1.3 76.9 - - - +
47B ILE* 1.3 62.4 + - - +
95B LYS* 6.1 0.4 - - - +
108B THR* 6.0 4.8 - - - -
109B VAL 3.7 3.4 - - - +
110B GLU* 3.2 38.7 + - + +
208B GLY* 3.5 1.6 - - - -
209B LEU* 2.7 52.5 + - + +
375B SER* 3.6 35.5 - - - -
376B GLU* 3.4 49.9 + - - +
379B LEU* 3.8 20.8 - - + +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER 5.3 0.7 - - - -
46B ARG* 1.3 84.7 - - - +
48B GLY* 1.3 61.8 + - - +
107B TYR 3.7 0.7 - - - +
108B THR* 3.3 2.5 - - - -
109B VAL* 2.8 53.6 + - + +
111B CYS* 6.5 1.1 - - - -
116B VAL* 5.0 9.6 - - + +
119B LEU* 6.3 0.2 - - + -
120B MET* 4.1 27.6 - - + -
123B LEU* 4.3 9.5 - - + +
206B LEU* 3.9 22.4 - - + -
207B ILE 3.4 9.4 - - - +
208B GLY* 4.0 2.5 - - - -
209B LEU 4.4 0.2 - - - +
211B VAL* 3.5 40.6 - - + -
216B LEU* 4.3 3.8 - - + -
379B LEU* 4.4 2.5 - - - -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 1.3 76.7 - - - +
49B LEU* 1.3 60.4 + - - -
50B PHE* 3.7 14.2 - - - -
107B TYR 3.1 7.6 - - - -
108B THR* 3.9 14.4 - - - -
123B LEU* 5.1 0.2 - - - -
205B ALA 3.6 1.4 - - - +
206B LEU* 3.7 5.6 - - - +
207B ILE 2.8 35.1 + - - +
379B LEU* 4.0 4.5 - - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 1.3 72.3 - - - -
50B PHE* 1.3 60.1 + - - +
51B ILE* 3.8 16.3 + - + +
105B MET 3.7 1.4 - - - +
106B ALA* 3.5 1.4 - - - -
107B TYR* 2.7 38.4 + - + +
123B LEU* 4.4 14.5 - - + +
124B LEU* 5.4 0.9 - - + -
127B THR* 3.6 35.2 - - + +
128B THR* 5.5 0.2 - - + -
204B MET* 3.9 31.6 - - + -
205B ALA 3.4 23.8 - - - +
206B LEU* 4.0 11.0 - - + -
224B LEU* 4.0 23.1 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 3.7 20.0 - - - -
49B LEU* 1.3 74.1 - - - +
51B ILE* 1.3 60.8 + - - +
104B ASN* 5.3 5.2 - - + -
105B MET 3.6 2.5 - - - -
106B ALA* 3.7 24.5 - - + -
108B THR* 4.8 4.3 - - + -
204B MET* 3.4 4.3 - - - +
205B ALA* 2.8 37.4 + - + +
207B ILE* 3.6 27.1 - - + -
379B LEU* 3.4 28.5 - - + -
380B ASP* 3.9 24.9 - - + -
383B GLY* 3.7 28.9 - - - +
384B SER* 4.2 3.4 - - - -
387B LEU* 3.6 19.3 - - + +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.9 19.1 - - + +
50B PHE* 1.3 81.0 - - - +
52B LYS* 1.3 62.5 + - - +
53B ALA* 2.9 17.7 + - + -
104B ASN* 3.2 3.5 - - - -
105B MET* 2.7 43.3 + - + +
107B TYR* 4.0 19.1 - - + -
127B THR* 4.9 0.2 - - + -
198B HIS 3.4 24.0 - - - +
199B PHE* 3.3 42.6 - - + -
203B ARG 3.5 7.0 - - - +
204B MET* 3.7 15.7 - - + -
387B LEU* 3.8 5.5 - - - +
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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