Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 1SQG
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 MET 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO 3.7 1.8 + - - -
173A PRO* 1.3 70.3 - - - +
175A TRP* 1.3 61.5 + - - +
176A LEU* 3.9 15.2 + - + -
209A VAL 3.8 0.7 - - - +
210A ARG* 3.7 1.8 - - - -
211A LEU* 3.0 51.2 + - + +
214A PRO* 4.0 31.7 - - + +
215A ALA 3.3 37.9 - - - +
217A VAL* 6.1 2.2 - - + -
220A LEU* 5.4 2.5 - - - -
230A VAL* 4.7 19.3 - - + -
333A ARG* 4.9 2.9 - - - +
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Residues in contact with TRP 175 (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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173A PRO* 3.4 15.3 + - + +
174A MET* 1.3 75.1 - - - +
176A LEU* 1.3 65.3 + - - +
200A PHE 4.5 2.7 - - - -
201A PRO 5.0 1.8 - - - -
202A HIS* 3.7 30.5 - + + -
208A ALA* 3.8 26.7 - - + -
209A VAL 3.5 19.1 - - - -
210A ARG* 3.5 35.2 - - + -
230A VAL* 3.7 7.4 - - - +
231A GLN 3.1 36.9 + - - +
232A ASP* 3.3 26.0 - - - -
233A ALA* 3.5 18.8 - - + +
236A GLN* 4.5 0.4 - - - +
333A ARG* 3.7 12.5 - - - +
416A GLU 3.6 26.2 - - - -
417A GLU* 2.9 24.7 + - - -
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Residues in contact with LEU 176 (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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174A MET* 4.1 12.8 - - + +
175A TRP* 1.3 80.9 - - - +
177A ARG* 1.3 60.3 + - - +
178A ILE* 4.1 1.3 - - + -
188A TRP* 3.6 32.5 - - + -
208A ALA* 3.3 0.7 - - - +
209A VAL* 2.8 42.8 + - + +
211A LEU* 3.8 29.2 - - + -
220A LEU* 3.9 18.8 - - + -
228A VAL* 3.7 11.2 - - + -
229A THR 3.3 4.5 - - - +
230A VAL* 3.8 26.5 - - + -
231A GLN 4.4 0.7 - - - -
236A GLN* 3.0 12.2 - - - +
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Residues in contact with ARG 177 (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 LEU* 1.3 75.1 - - - +
178A ILE* 1.3 63.8 + - - +
179A ASN 3.6 0.7 + - - -
207A ASP* 3.4 12.1 - - + -
228A VAL* 3.4 2.9 - - - -
229A THR* 2.7 60.9 + - - +
231A GLN* 2.8 32.6 + - + +
236A GLN* 3.5 21.8 - - - +
259A GLY 2.8 21.2 + - - -
262A THR* 2.9 25.5 + - - -
263A HIS* 3.4 32.2 + - - +
266A GLU* 2.8 39.5 + - - +
293A LEU* 3.9 0.6 - - - +
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Residues in contact with ILE 178 (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 LEU* 4.5 1.6 - - + -
177A ARG* 1.3 76.6 - - - +
179A ASN* 1.3 61.9 + - - +
180A ARG* 3.1 8.5 + - - -
183A HIS* 3.8 21.8 - - + +
184A SER 3.9 5.8 - - - +
185A ARG* 4.0 14.6 - - + +
188A TRP* 3.4 58.8 - - + -
207A ASP* 2.7 36.3 + - - +
209A VAL* 3.8 24.5 - - + -
227A TRP 3.8 4.7 - - - +
228A VAL* 3.8 11.4 - - + -
266A GLU* 3.9 5.1 - - - +
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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