Contacts of the helix formed by residues 162 - 179 (chain A) in PDB entry 1F7U
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 HIS 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 4.8 6.5 + - - -
152A PRO* 3.8 34.6 - - + +
153A ASN 5.1 2.2 + - - -
156A LYS* 5.4 8.2 + - + +
157A PRO 4.0 11.0 - - - -
158A PHE* 3.6 29.5 - + + -
159A HIS* 3.0 60.9 + + - +
161A GLY* 1.3 73.7 - - - +
163A LEU* 1.3 62.7 + - - +
164A ARG 3.3 0.4 + - - -
165A SER* 4.0 5.4 + - - -
166A THR* 2.8 26.2 + - - -
418A LEU* 5.7 0.2 - - + -
800A ARG 5.3 3.8 + - - -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A HIS 3.9 2.0 + - - -
160A ALA* 3.3 15.0 + - - +
161A GLY 3.1 0.4 - - - -
162A HIS* 1.3 78.7 - - - +
164A ARG* 1.3 62.9 + - - +
166A THR* 3.2 7.2 + - - -
167A ILE* 3.0 47.2 + - + +
284A LEU* 4.3 17.5 - - + -
418A LEU* 4.0 27.9 - - + +
422A LEU* 5.8 1.1 - - + -
458A VAL* 3.5 41.7 - - + +
459A MET* 4.9 4.0 - - + -
461A GLN* 4.2 5.4 - - - +
462A ASP* 4.1 17.7 - - + +
471A TYR* 4.5 2.7 - - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ALA 4.9 0.4 - - - +
161A GLY 3.6 12.3 - - - +
162A HIS 3.3 0.6 - - - -
163A LEU* 1.3 76.4 - - - +
165A SER* 1.3 65.6 + - - +
167A ILE* 3.7 4.0 - - - +
168A ILE* 3.0 35.0 + - + +
402A PHE* 3.6 25.3 - - + +
403A GLY 3.0 30.8 + - - +
405A VAL* 3.9 22.0 - - + -
462A ASP* 3.0 51.6 + - - +
465A GLY 5.2 0.4 + - - -
466A LYS 4.6 3.6 + - - -
467A ARG* 3.2 27.6 + - - +
469A ASN 3.0 23.0 + - - -
471A TYR* 3.8 13.0 - - - -
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Residues in contact with SER 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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149A PHE* 3.4 8.1 - - - +
150A SER* 2.6 38.4 + - - -
161A GLY 4.7 0.4 + - - -
162A HIS* 4.0 4.5 + - - -
163A LEU 3.7 0.2 - - - -
164A ARG* 1.3 76.7 - - - +
166A THR* 1.3 63.0 + - - +
169A GLY 3.0 19.1 + - - -
370A VAL* 2.9 25.9 + - - +
371A ILE* 5.5 0.2 - - - -
402A PHE* 3.6 29.5 - - - -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.4 12.2 - - - -
150A SER* 3.1 19.0 + - - -
158A PHE* 4.5 4.4 - - + -
162A HIS 2.8 19.4 + - - -
163A LEU* 3.2 11.8 + - - -
164A ARG 3.1 0.6 - - - -
165A SER* 1.3 78.2 - - - +
167A ILE* 1.3 58.3 + - - +
170A GLY 3.0 21.1 + - - -
281A TYR* 3.7 24.3 - - + -
284A LEU* 3.8 18.2 - - + -
286A ILE* 3.4 24.7 - - + +
288A TYR* 4.8 0.2 - - - +
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Residues in contact with ILE 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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163A LEU* 3.0 42.3 + - + +
164A ARG 3.7 4.3 - - - +
166A THR* 1.3 72.4 - - + +
168A ILE* 1.3 64.3 + - + +
170A GLY* 4.3 1.8 - - - +
171A PHE* 2.9 29.1 + - - +
284A LEU* 4.3 15.0 - - + -
286A ILE* 4.9 2.7 - - + -
459A MET* 3.9 42.0 - - + +
462A ASP* 3.7 34.3 - - + +
463A MET* 3.8 26.1 - - + +
599A LEU 4.6 1.4 - - - +
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Residues in contact with ILE 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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164A ARG* 3.0 32.8 + - + +
167A ILE* 1.3 81.0 - - + +
169A GLY* 1.3 60.2 + - - +
171A PHE* 3.3 5.4 + - - +
172A LEU* 2.9 43.0 + - + +
370A VAL* 3.8 17.0 - - + -
400A VAL* 4.4 2.9 - - + -
401A ASN 4.9 0.2 - - - +
402A PHE* 3.7 36.8 - - + -
462A ASP* 5.0 3.8 - - - +
463A MET* 6.0 0.7 - - + -
467A ARG* 3.7 32.8 - - + +
545A HIS 5.1 0.4 - - - +
547A PRO* 4.5 15.3 - - + -
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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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147A ILE* 4.2 5.5 - - - +
149A PHE* 3.5 34.4 - - - -
165A SER 3.0 9.5 + - - -
168A ILE* 1.3 76.3 - - - +
170A GLY* 1.3 58.1 + - - +
172A LEU* 3.3 3.0 + - - +
173A ALA* 2.9 30.8 + - - +
370A VAL* 4.0 12.1 - - - +
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Residues in contact with GLY 170 (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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149A PHE* 3.5 13.9 - - - -
166A THR 3.0 17.2 + - - -
167A ILE* 3.9 1.6 - - - -
168A ILE 3.3 0.4 - - - -
169A GLY* 1.3 75.1 - - - +
171A PHE* 1.3 63.6 + - - +
173A ALA* 3.3 4.6 + - - +
174A ASN* 3.0 31.9 + - - +
185A ARG* 5.1 1.7 + - - -
286A ILE* 4.2 14.1 - - - -
599A LEU 5.5 0.7 - - - -
600A GLY* 6.2 0.7 - - - -
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE 2.9 18.8 + - - +
168A ILE* 3.5 4.7 - - + +
170A GLY* 1.3 75.5 - - - +
172A LEU* 1.3 88.2 + - + +
174A ASN* 3.1 5.4 + - - +
175A LEU* 2.8 43.4 + - + +
463A MET* 4.0 11.9 - - + -
541A ALA* 4.3 2.0 - - + -
545A HIS 4.4 1.6 - - - -
546A GLU 3.8 17.5 - - - -
547A PRO* 3.6 31.6 - - + -
550A VAL* 3.9 25.1 - - + -
598A LEU* 3.8 31.2 - - + +
599A LEU* 3.7 22.7 + - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.9 12.1 - - + -
168A ILE* 2.9 35.3 + - + +
169A GLY* 3.7 4.3 - - - +
171A PHE* 1.3 97.2 - - + +
173A ALA* 1.3 57.9 + - - +
175A LEU* 4.2 8.3 - - + -
176A TYR* 2.9 41.0 + - + -
368A ILE* 4.4 8.5 - - + -
370A VAL* 4.2 17.9 - - + -
400A VAL* 4.2 22.0 - - + -
545A HIS* 3.8 35.4 - - + +
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Residues in contact with ALA 173 (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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147A ILE* 3.6 13.4 - - + +
149A PHE* 4.8 2.9 - - + -
169A GLY 2.9 17.4 + - - +
170A GLY* 3.5 5.4 - - - +
172A LEU* 1.3 76.3 - - - +
174A ASN* 1.3 64.8 + - - +
176A TYR 3.5 0.2 + - - -
177A GLU* 3.2 28.9 + - - +
183A VAL* 3.8 7.9 - - + +
185A ARG* 3.3 43.1 - - + +
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Residues in contact with ASN 174 (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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170A GLY 3.0 19.3 + - - +
171A PHE 3.1 2.0 + - - +
173A ALA* 1.3 77.0 - - - +
175A LEU* 1.3 56.7 + - - +
177A GLU* 3.8 5.2 - - - +
178A LYS* 3.0 31.4 + - - +
185A ARG* 3.0 21.9 + - - +
285A ASN* 5.6 4.6 + - - +
597A ARG 3.5 13.4 + - - -
598A LEU* 3.0 39.8 + - + +
600A GLY* 4.2 8.9 - - - +
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Residues in contact with LEU 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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171A PHE* 2.8 31.8 + - + +
172A LEU* 3.7 12.3 - - + +
174A ASN* 1.3 77.4 - - - +
176A TYR* 1.3 63.7 + - + +
178A LYS* 3.3 5.1 + - + +
179A LEU* 3.1 27.7 + - + +
538A LEU* 3.8 28.5 - - + +
541A ALA* 3.5 15.9 - - + +
542A ILE* 3.5 42.0 - - + +
598A LEU* 3.6 26.0 - - + +
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Residues in contact with TYR 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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145A VAL* 3.9 10.8 - - + -
147A ILE* 4.3 5.2 - - + -
172A LEU* 2.9 34.4 + - + +
175A LEU* 1.3 74.5 - - + +
177A GLU* 1.3 65.8 + - - +
179A LEU 3.2 8.1 + - - -
180A GLY 3.4 0.3 + - - -
181A TRP* 3.0 61.9 + + + +
183A VAL* 3.6 18.2 - - + -
366A LYS* 3.5 27.6 - - + -
368A ILE* 3.6 15.4 - - + +
542A ILE* 3.7 31.8 + - + +
545A HIS* 2.7 39.4 + + - -
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Residues in contact with GLU 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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138A LYS* 5.2 5.9 + - - -
173A ALA 3.2 14.6 + - - +
174A ASN* 3.8 6.8 - - - +
176A TYR* 1.3 76.1 - - - +
178A LYS* 1.3 65.0 + - - +
180A GLY* 3.1 14.0 + - - -
181A TRP 3.6 12.6 + - - +
183A VAL* 3.5 24.1 + - + +
185A ARG* 2.8 41.0 + - - -
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Residues in contact with LYS 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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132A GLU* 3.0 33.6 + - - +
133A ASP* 4.0 9.1 + - - +
135A GLY 5.8 0.4 - - - +
136A SER* 3.0 53.6 - - - +
137A CYS 3.2 6.1 + - - +
174A ASN 3.0 19.4 + - - +
175A LEU* 3.5 6.7 - - + +
177A GLU* 1.3 76.8 - - - +
179A LEU* 1.3 59.8 + - + +
180A GLY 3.4 0.2 - - - -
538A LEU* 4.0 24.7 - - + -
594A ASN* 6.4 0.9 - - - -
598A LEU* 4.3 15.9 - - + -
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Residues in contact with LEU 179 (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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135A GLY 3.9 20.2 - - - +
136A SER* 4.3 0.2 - - - -
137A CYS* 3.2 30.0 - - + +
139A LEU* 3.9 16.1 - - - +
175A LEU* 3.1 20.2 + - + +
176A TYR 3.2 5.8 + - - +
177A GLU 3.1 0.6 - - - -
178A LYS* 1.3 83.9 - - + +
180A GLY* 1.3 56.2 + - - +
181A TRP* 3.6 5.9 + - + -
535A PRO 6.0 0.4 - - - +
538A LEU* 3.8 33.7 - - + +
539A ARG* 4.4 5.4 - - + +
542A ILE* 3.7 37.5 - - + -
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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
------------------------------------------------------------
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