Contacts of the helix formed by residues 158 - 174 (chain A) in PDB entry 2XFN
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 THR 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ILE* 4.4 13.9 - - + -
111A THR* 4.0 30.8 - - - +
114A ASP* 2.7 35.8 + - + +
156A CYS* 3.8 4.1 - - - +
157A TRP* 1.3 85.5 - - + +
159A GLU* 1.3 66.2 + - - +
160A SER* 3.7 4.9 + - - -
161A ALA* 3.1 15.9 + - - +
162A LYS* 3.2 19.7 + - - +
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Residues in contact with GLU 159 (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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158A THR* 1.3 74.0 - - - +
160A SER* 1.3 55.2 + - - +
162A LYS* 3.1 39.9 + - - +
163A GLN* 2.8 52.1 + - + +
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Residues in contact with SER 160 (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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106A VAL* 5.4 0.5 - - - +
111A THR* 3.8 18.0 - - - +
115A HIS* 2.9 20.5 + - - -
158A THR* 3.2 3.3 - - - -
159A GLU* 1.3 77.4 - - - +
161A ALA* 1.3 62.8 + - - +
163A GLN* 3.5 6.5 + - - +
164A LEU* 3.1 23.6 + - - +
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Residues in contact with ALA 161 (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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114A ASP* 3.1 30.7 - - - +
115A HIS* 3.3 30.7 + - + +
118A PHE* 5.0 6.3 - - + -
156A CYS* 4.0 11.7 - - - -
158A THR* 3.1 5.7 + - - +
160A SER* 1.3 76.3 - - - +
162A LYS* 1.3 61.7 + - - +
164A LEU* 3.3 2.0 + - - +
165A ALA* 2.8 32.2 + - - +
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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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152A LEU* 4.3 19.5 - - + -
153A ASP* 2.9 40.1 + - - +
156A CYS* 3.8 22.8 + - + -
158A THR 3.2 9.6 + - - +
159A GLU* 3.1 37.9 + - - +
161A ALA* 1.3 79.0 - - - +
163A GLN* 1.3 61.6 + - - +
165A ALA* 3.8 2.9 - - - +
166A THR* 2.8 38.3 + - - +
1502A C15 5.8 3.6 - - - -
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Residues in contact with GLN 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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92A VAL* 5.9 1.8 - - + -
159A GLU* 2.8 39.0 + - + +
160A SER* 3.8 5.6 - - - +
162A LYS* 1.3 80.6 - - - +
164A LEU* 1.3 61.9 + - - +
166A THR* 3.3 11.4 + - - +
167A LEU* 3.1 22.0 + - - +
318A ASP* 3.3 37.0 - - - +
319A GLY* 5.6 1.2 - - - -
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Residues in contact with LEU 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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90A HIS* 4.0 27.1 - - + +
103A PHE* 5.1 1.6 - - + -
104A PRO* 4.4 23.1 - - + +
115A HIS* 4.0 24.2 - - + +
119A TRP* 3.9 24.0 - - + +
160A SER 3.1 15.4 + - - +
161A ALA 3.9 2.7 - - - +
163A GLN* 1.3 76.4 - - - +
165A ALA* 1.3 61.2 + - - +
167A LEU* 3.2 8.3 + - + +
168A PHE* 2.9 27.2 + - - +
316A ILE* 4.3 9.0 - - + -
318A ASP* 4.6 2.6 + - - +
1501A XCG 3.5 30.1 - - + -
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Residues in contact with ALA 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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118A PHE* 3.3 38.3 - - + -
119A TRP* 4.9 1.0 - - - -
152A LEU* 3.6 21.8 - - + -
156A CYS* 4.5 0.2 - - - -
161A ALA 2.8 18.9 + - - +
162A LYS* 3.8 2.5 - - - +
164A LEU* 1.3 77.2 - - - +
166A THR* 1.3 56.9 + - - +
168A PHE* 3.3 10.0 + - - +
169A VAL* 3.0 32.1 + - - +
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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
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152A LEU* 3.6 11.1 - - - +
162A LYS* 2.8 26.3 + - - +
163A GLN* 3.5 12.1 + - - +
164A LEU 3.2 0.2 - - - -
165A ALA* 1.3 74.1 - - - +
167A LEU* 1.3 66.0 + - - +
169A VAL* 3.2 2.9 + - - +
170A ASN* 3.0 42.5 + - - +
176A GLU* 5.7 2.5 - - - +
177A THR* 4.0 23.4 + - + +
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Residues in contact with LEU 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 GLN 3.1 13.2 + - - +
164A LEU* 3.2 12.3 + - + +
166A THR* 1.3 76.4 - - - +
168A PHE* 1.3 62.5 + - - +
170A ASN* 3.3 9.9 + - + +
171A LEU* 2.9 28.7 + - + +
316A ILE* 3.8 17.0 - - + -
317A ILE 3.4 34.8 - - - +
318A ASP* 4.0 16.6 - - + +
325A ALA* 4.1 21.8 - - + +
1501A XCG 3.1 35.4 - - + -
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Residues in contact with PHE 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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118A PHE* 4.9 3.1 - + - -
119A TRP* 3.5 37.9 - + + -
122A MET* 4.3 10.3 - - + -
164A LEU 2.9 14.6 + - - +
165A ALA 3.3 11.4 - - - +
167A LEU* 1.3 75.8 - - - +
169A VAL* 1.3 64.8 + - + +
171A LEU* 3.9 2.2 - - + +
172A CYS* 3.0 41.1 + - - -
185A PHE* 3.5 30.7 - + - -
189A VAL* 4.0 8.7 - - + -
195A THR* 4.2 9.2 - - + -
198A ILE* 3.8 15.9 - - + -
199A ILE* 2.9 36.8 - - + -
1501A XCG 3.7 16.7 - + + -
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Residues in contact with VAL 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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118A PHE* 6.1 0.2 - - + -
122A MET* 5.6 0.2 - - + -
148A MET* 4.0 16.8 - - + -
152A LEU* 4.9 2.0 - - + -
165A ALA* 3.0 18.3 + - + +
166A THR 3.2 5.8 + - - +
168A PHE* 1.3 76.7 - - + +
170A ASN* 1.3 66.2 + - - +
172A CYS* 3.3 1.2 + - - -
173A VAL* 3.1 39.7 + - + +
175A ALA 4.1 8.7 - - - +
177A THR* 3.8 31.9 - - + -
180A VAL* 4.4 9.2 - - + -
185A PHE* 3.8 33.9 - - + -
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Residues in contact with ASN 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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166A THR* 3.0 36.5 + - - +
167A LEU* 3.7 8.1 - - + +
169A VAL* 1.3 79.5 - - - +
171A LEU* 1.3 56.3 + - - +
174A THR* 2.9 28.8 + - - -
175A ALA 3.0 23.9 + - - +
176A GLU* 3.7 25.4 + - - +
177A THR* 4.0 6.5 - - - +
325A ALA* 6.2 0.7 - - + -
345A LEU* 3.7 25.4 - - + +
346A ALA* 5.1 3.1 - - + -
347A HIS* 6.1 0.5 - - - -
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Residues in contact with LEU 171 (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 LEU* 2.9 19.5 + - + +
168A PHE* 3.9 2.7 - - - +
170A ASN* 1.3 75.1 - - - +
172A CYS* 1.3 67.1 + - - +
199A ILE* 6.5 0.9 - - + -
326A TYR* 3.5 50.7 - - + -
343A PHE* 3.8 24.7 - - + -
345A LEU* 3.8 15.7 - - + +
398A TYR* 2.8 30.1 + - - +
1501A XCG 3.6 25.6 - - + -
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Residues in contact with CYS 172 (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 PHE* 3.0 55.8 + - - +
169A VAL 3.3 2.7 + - - +
171A LEU* 1.3 79.2 - - - +
173A VAL* 1.3 67.0 + - + +
185A PHE* 3.9 16.2 - - + -
188A TYR* 4.0 9.9 + - - -
198A ILE* 3.9 31.4 - - + -
199A ILE* 5.1 1.6 - - - -
398A TYR* 3.4 18.3 - - - -
435A TYR* 5.1 4.0 + - - -
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Residues in contact with VAL 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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169A VAL* 3.1 27.4 + - + +
172A CYS* 1.3 82.5 - - - +
174A THR* 1.3 77.4 + - - +
175A ALA* 3.0 19.3 + - + +
180A VAL* 4.5 1.6 - - + -
184A TRP* 3.5 35.0 - - + -
185A PHE* 3.8 25.4 - - + -
188A TYR* 3.6 26.9 - - + -
292A GLY* 4.3 4.3 + - - -
398A TYR* 4.6 3.1 - - - -
399A THR* 5.1 8.9 - - + +
401A TYR* 4.8 4.0 - - - +
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Residues in contact with THR 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 ASN 2.9 14.6 + - - -
173A VAL* 1.3 84.8 + - - +
175A ALA* 1.3 55.9 + - - +
292A GLY* 3.3 8.7 - - - -
293A SER* 3.0 35.4 + - - +
294A VAL* 3.7 16.4 - - + -
345A LEU* 3.8 9.6 - - + -
346A ALA* 3.8 11.2 - - - +
350A ARG* 5.0 1.4 + - - -
397A CYS 2.6 20.9 + - - +
398A TYR* 3.3 47.7 + - + +
399A THR 4.9 0.2 + - - -
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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