Contacts of the strand formed by residues 193 - 200 (chain A) in PDB entry 3FZM
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 ARG 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 5.3 2.9 - - - +
188A LYS* 3.5 42.5 - - + +
191A ALA 4.0 9.6 - - - +
192A GLU* 1.3 76.0 - - - +
194A ASN* 1.3 62.6 + - - +
195A VAL* 4.0 8.2 + - + -
210A LEU 3.8 0.2 - - - +
211A THR* 3.3 7.3 - - - +
212A ILE* 2.8 43.9 + - + +
332A HIS* 3.3 32.1 + - + +
333A ASP* 2.7 50.1 + - - +
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Residues in contact with ASN 194 (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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192A GLU* 4.6 10.2 + - - +
193A ARG* 1.3 72.4 + - - +
195A VAL* 1.3 62.0 + - - +
209A ILE* 4.7 0.4 - - + -
210A LEU 3.4 6.4 + - - +
211A THR* 3.3 23.2 + - - -
220A LYS* 4.4 4.6 - - - +
326A LEU* 3.6 28.4 - - + +
330A GLN* 2.8 27.4 - - - +
331A ILE* 3.6 17.4 - - + -
332A HIS* 2.8 47.1 + - - -
333A ASP 3.4 4.0 + - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA* 4.9 0.7 - - + -
185A LEU* 3.4 27.8 - - + -
193A ARG* 4.6 4.3 - - + -
194A ASN* 1.3 77.2 - - - +
196A LEU* 1.3 62.5 + - - +
197A ILE* 3.9 13.6 + - + +
208A SER 3.6 0.7 - - - +
209A ILE* 3.2 5.9 - - - -
210A LEU* 2.9 39.6 + - + +
212A ILE* 3.4 37.7 - - + -
331A ILE* 4.5 2.0 - - - -
333A ASP* 3.3 22.7 - - + +
335A VAL* 4.0 14.1 - - + -
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Residues in contact with LEU 196 (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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195A VAL* 1.3 72.5 - - - +
197A ILE* 1.3 65.6 + - - +
198A PHE* 3.9 24.1 + - + -
207A VAL* 4.1 15.7 - - + -
208A SER 3.5 7.4 - - - +
209A ILE* 3.7 26.5 - - + -
317A VAL* 4.0 22.0 - - + +
321A LEU* 4.7 1.8 - - + -
331A ILE* 3.9 16.4 - - + +
333A ASP 2.7 12.5 + - - +
334A ILE* 3.2 18.0 - - + -
335A VAL* 2.8 26.7 + - - +
350A LEU* 4.8 0.7 - - + -
354A PHE* 3.8 26.9 - - + -
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Residues in contact with ILE 197 (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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176A PRO* 3.3 54.7 - - + +
179A ALA* 4.3 9.9 - - + -
180A ALA* 4.0 8.1 - - + +
195A VAL* 4.0 14.1 - - + +
196A LEU* 1.3 75.4 - - - +
198A PHE* 1.3 61.6 + - - +
199A ASP* 4.9 7.0 - - + +
206A ASP 3.6 2.1 - - - +
207A VAL* 3.4 7.1 - - - +
208A SER* 2.7 39.3 + - - +
210A LEU* 4.5 8.3 - - + -
335A VAL* 3.5 35.9 - - + +
337A VAL* 4.5 11.2 - - + -
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Residues in contact with PHE 198 (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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196A LEU* 3.9 12.0 + - + -
197A ILE* 1.3 71.4 - - - +
199A ASP* 1.3 59.0 + - - +
200A LEU* 3.9 8.1 - - + -
205A PHE* 3.5 35.7 - + - -
206A ASP 4.0 1.6 - - - -
207A VAL* 4.6 2.7 - - + +
313A THR* 3.9 22.2 - - + -
314A LEU* 5.6 1.3 - - + -
317A VAL* 4.0 15.3 - - + -
334A ILE* 4.8 0.9 - - + -
335A VAL 2.9 14.3 + - - +
336A LEU* 3.7 6.9 - - + -
337A VAL 3.1 22.5 + - - +
341A THR* 3.7 23.6 - - + -
346A ILE* 3.9 23.8 - - + -
350A LEU* 3.7 38.1 - - + -
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Residues in contact with ASP 199 (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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175A GLU* 4.7 12.4 - - - +
197A ILE* 4.9 8.3 - - + +
198A PHE* 1.3 71.5 - - - +
200A LEU* 1.3 62.7 + - - +
201A GLY* 4.4 4.7 + - - -
204A THR* 4.5 6.6 + - - +
205A PHE* 3.2 6.3 - - - -
206A ASP* 2.7 60.1 + - + +
337A VAL* 3.0 36.1 - - + +
338A GLY* 4.8 1.9 - - - -
369A VAL* 4.7 4.5 - - - +
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Residues in contact with LEU 200 (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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198A PHE* 3.9 20.5 + - + -
199A ASP* 1.3 74.3 - - - +
201A GLY* 1.3 58.0 + - - +
204A THR 3.6 0.7 - - - -
205A PHE* 3.5 37.2 - - + -
228A LEU* 3.8 28.7 - - + +
229A GLY* 4.5 2.2 - - - -
233A PHE* 4.3 8.5 - - + -
313A THR* 4.3 7.9 - - + -
337A VAL 2.8 8.9 + - - -
338A GLY* 3.1 23.1 - - - +
340A SER* 3.2 27.5 + - - -
341A THR* 3.8 3.7 + - + +
346A ILE* 3.6 30.3 - - + -
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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