Contacts of the strand formed by residues 161 - 169 (chain A) in PDB entry 1QFG
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 LEU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A THR* 4.2 10.3 - - + +
159A GLU* 4.7 0.9 - - - +
160A PRO* 1.3 78.1 - - - +
162A LYS* 1.3 69.1 + - - +
163A GLU* 4.5 4.3 - - + +
179A ASP* 3.4 30.3 - - + +
180A PHE* 3.1 4.9 - - - +
181A SER* 2.9 43.1 + - - +
193A ARG* 3.7 32.1 - - - +
724A ARG* 3.6 44.4 - - - +
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Residues in contact with LYS 162 (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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160A PRO* 5.1 10.9 - - + +
161A LEU* 1.3 80.3 - - - +
163A GLU* 1.3 57.8 + - - +
180A PHE* 3.1 27.6 - - + -
181A SER 6.2 0.2 - - - -
182A ASP* 4.4 17.0 + - - -
192A TYR* 6.0 1.6 - - - -
723A PHE 3.6 0.3 - - - +
724A ARG* 3.3 4.7 - - - +
725A PHE* 2.8 70.3 + - + +
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Residues in contact with GLU 163 (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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124A TYR* 2.6 34.8 + - - +
154A LYS* 5.0 0.7 + - - -
161A LEU* 4.5 3.8 - - + -
162A LYS* 1.3 74.3 - - - +
164A VAL* 1.3 73.9 + - - +
165A GLN* 4.8 2.7 + - - -
178A PHE* 3.2 9.1 - - - +
179A ASP* 3.0 47.0 + - + +
180A PHE* 3.5 3.7 - - - -
722A THR* 4.2 16.9 + - - +
723A PHE 3.3 9.6 - - - +
724A ARG* 2.7 44.7 + - - +
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Residues in contact with VAL 164 (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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162A LYS 5.7 0.2 - - - -
163A GLU* 1.3 80.6 - - - +
165A GLN* 1.3 61.6 + - - +
166A PHE* 3.4 37.7 - - + -
176A THR* 5.5 0.9 - - - +
177A GLY 3.4 7.9 - - - +
178A PHE* 4.6 4.7 - - + -
180A PHE* 4.1 17.3 - - + -
721A ALA 4.0 0.3 - - - +
722A THR* 3.5 1.0 - - - -
723A PHE* 2.6 46.7 + - + +
725A PHE* 5.2 19.3 - - + -
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Residues in contact with GLN 165 (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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62A GLN* 4.2 16.6 + - - +
124A TYR* 3.8 36.0 - - + +
163A GLU* 4.8 4.7 + - - +
164A VAL* 1.3 77.4 - - - +
166A PHE* 1.3 70.4 + - - +
167A LYS* 4.1 15.5 - - + -
175A GLN* 4.3 8.0 + - - -
176A THR* 3.6 4.2 + - - -
177A GLY* 2.8 41.2 + - - +
720A THR* 3.6 19.4 - - + +
721A ALA 3.2 3.8 - - - -
722A THR* 3.4 34.2 + - - +
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Residues in contact with PHE 166 (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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164A VAL* 3.4 28.5 - - + -
165A GLN* 1.3 75.5 - - - +
167A LYS* 1.3 61.8 - - - +
175A GLN 3.4 3.8 - - - -
176A THR* 3.5 27.6 - - - -
720A THR* 3.1 4.9 - - - +
721A ALA* 2.6 38.7 + - + +
723A PHE* 3.9 34.5 - + - -
1104A GOL 3.9 22.2 - - - +
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Residues in contact with LYS 167 (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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62A GLN* 2.5 38.5 + - - +
165A GLN* 4.1 9.4 - - + +
166A PHE* 1.3 74.1 - - - +
168A ALA* 1.3 58.4 + - - +
173A LEU* 4.4 9.0 - - + -
174A PHE* 3.4 7.1 - - - -
175A GLN* 2.9 73.5 + - + +
199A ARG* 5.7 0.9 - - - +
718A VAL* 4.1 16.6 - - + +
719A ALA 3.2 6.7 - - - +
720A THR* 2.9 33.6 + - + +
1104A GOL 3.0 8.8 + - - -
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Residues in contact with ALA 168 (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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167A LYS* 1.3 72.9 - - - +
169A GLY* 1.3 56.1 + - - +
173A LEU* 3.3 5.8 - - - -
174A PHE* 4.2 16.8 - - + -
718A VAL* 3.6 2.4 - - - -
719A ALA* 2.7 38.0 + - + +
1104A GOL 3.2 28.6 + - - +
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Residues in contact with GLY 169 (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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168A ALA* 1.3 74.8 - - - +
170A THR* 1.3 67.4 + - - +
172A SER* 3.6 5.2 + - - -
173A LEU* 2.8 31.0 + - - +
174A PHE* 5.6 1.9 - - - -
717A VAL 3.0 13.2 - - - -
718A VAL* 4.0 4.3 - - - -
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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