Contacts of the strand formed by residues 161 - 169 (chain A) in PDB entry 4JF7
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 CYS 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 4.7 1.0 - - - +
159A GLU 4.4 0.2 - - - +
160A GLY* 1.3 75.0 - - - +
162A THR* 1.3 65.1 + - - +
163A ARG* 3.7 19.7 - - - -
179A ASN 3.6 0.3 - - - +
180A VAL* 3.4 4.9 - - - +
181A ILE* 2.8 52.1 + - + +
184A GLY 4.0 1.6 - - - -
185A CYS* 2.1 60.6 - - - +
552A GLN* 5.1 0.2 - - + -
553A PHE* 4.0 7.0 - - - -
147B ASN* 4.8 1.2 - - - +
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Residues in contact with THR 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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153A PRO 4.1 13.8 + - - +
154A THR* 4.9 1.7 - - - -
155A ALA* 4.8 15.3 - - + +
161A CYS* 1.3 78.4 - - - +
163A ARG* 1.3 71.5 + - - +
178A HIS* 3.7 33.5 - - + +
179A ASN 3.2 4.0 - - - +
180A VAL* 4.6 9.9 - - + -
544A GLU* 4.4 0.2 - - - +
553A PHE* 3.2 24.4 + - - +
554A GLN* 3.7 1.2 - - - +
555A ILE* 3.6 29.3 + - - +
147B ASN* 6.3 0.2 - - - +
149B PRO* 6.4 2.0 - - + -
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Residues in contact with ARG 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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161A CYS* 3.7 18.6 - - - -
162A THR* 1.3 81.9 - - - +
164A ILE* 1.3 89.8 + - + +
165A PRO 3.7 1.1 - - - -
178A HIS* 3.6 1.2 - - - +
179A ASN* 2.8 38.5 + - + +
181A ILE* 4.9 10.3 - - + -
185A CYS* 4.5 8.2 + - + +
495A ARG* 4.7 7.4 - - - +
522A ALA* 4.0 9.1 - - - +
523A TYR* 3.9 14.8 + - - -
544A GLU* 2.7 41.4 + - - -
553A PHE* 4.0 28.1 - - - -
555A ILE* 4.0 4.0 - - - +
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Residues in contact with ILE 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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163A ARG* 1.3 104.7 - - + +
165A PRO* 1.3 70.2 - - - +
166A SER 3.8 0.2 + - - -
177A THR 3.7 0.7 - - - +
178A HIS* 3.6 10.4 - - - -
179A ASN* 4.1 9.8 + - + +
193A GLN* 4.7 3.6 + - - -
225A LYS* 6.6 0.2 - - + -
226A SER* 4.5 14.4 - - - +
227A CYS 4.7 7.3 - - - +
291A THR* 3.6 36.6 - - + -
390A GLU* 5.3 0.4 - - - +
523A TYR* 3.5 29.8 - - + +
544A GLU* 2.7 14.1 + - - -
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Residues in contact with PRO 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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163A ARG 3.7 0.8 - - - -
164A ILE* 1.3 95.4 - - - +
166A SER* 1.3 62.6 + - - +
176A TYR* 3.7 26.2 - - + +
177A THR 3.2 7.9 - - - +
178A HIS* 3.9 2.9 - - + -
291A THR 3.6 4.0 - - - +
523A TYR* 4.7 3.8 - - + -
525A HIS* 3.1 44.6 + - + +
542A ILE* 4.0 21.8 - - + +
544A GLU* 3.7 18.8 - - + +
555A ILE* 3.8 10.1 - - + -
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Residues in contact with SER 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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165A PRO* 1.3 73.0 - - - +
167A PHE* 1.3 63.6 + - - +
176A TYR* 3.3 7.1 - - - -
177A THR* 2.8 50.2 + - - -
227A CYS 3.6 10.1 - - - -
228A SER* 3.4 0.7 - - - -
229A ILE* 3.0 24.4 + - - +
291A THR 2.7 24.3 + - - -
292A GLY 3.6 7.4 - - - -
293A SER 3.7 0.9 + - - -
525A HIS* 4.4 3.1 - - - -
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Residues in contact with PHE 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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151A PHE* 3.8 18.4 - + - -
165A PRO* 6.0 0.2 - - + -
166A SER* 1.3 78.2 + - - +
168A SER* 1.3 61.6 + - - +
169A LEU* 4.3 9.6 - - + -
174A TRP* 3.8 28.3 - + + -
175A CYS 3.2 17.3 - - - -
176A TYR* 3.8 16.8 - + + -
210A PHE* 3.7 28.3 - + - -
229A ILE* 4.2 0.4 - - - -
293A SER* 3.1 18.6 + - - -
392A ARG* 4.0 12.3 + - - +
525A HIS* 4.6 12.3 - - + -
527A THR* 3.7 35.7 - - + -
540A ILE* 4.5 7.2 - - + -
542A ILE* 3.6 26.9 - - + -
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Residues in contact with SER 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 PHE* 1.3 78.0 - - - +
169A LEU* 1.3 61.5 + - - +
170A THR* 5.1 1.9 - - - +
174A TRP* 3.1 5.2 - - - +
175A CYS* 2.7 41.1 + - - -
229A ILE* 3.7 9.8 - - - +
230A SER* 3.5 23.8 + - - -
231A THR* 3.0 26.5 + - - +
293A SER* 3.9 7.3 - - - -
294A GLY 4.0 5.5 + - - -
295A VAL* 5.7 0.2 - - - -
392A ARG* 5.7 0.7 - - - +
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Residues in contact with LEU 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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119A ASN* 3.8 7.2 - - - +
127A ILE* 3.7 28.2 - - + +
128A ASN* 3.7 12.8 + - - +
167A PHE* 4.3 14.2 - - + -
168A SER* 1.3 74.6 + - - +
170A THR* 1.3 81.7 + - - +
173A HIS 3.7 9.2 - - - +
174A TRP* 3.9 11.4 - - + -
200A ILE* 3.7 25.8 - - + -
210A PHE* 5.0 3.6 - - + -
392A ARG* 6.0 0.8 - - - +
527A THR* 4.1 18.3 - - + +
528A CYS 5.0 0.7 - - - +
529A PHE* 3.9 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