Contacts of the strand formed by residues 180 - 187 (chain D) in PDB entry 3SRF
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 ILE 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.9 24.0 - - + -
173D ILE 3.8 0.9 - - - +
174D TYR* 3.4 7.4 - - - +
175D VAL* 2.8 49.1 + - + +
176D ASP* 4.9 8.7 - - + +
179D LEU* 1.3 82.5 - - + +
181D SER* 1.3 62.2 + - - +
182D LEU* 4.2 11.4 - - + -
196D VAL* 5.0 0.7 - - + -
198D ASN* 3.6 11.4 - - - +
199D GLY 3.8 13.7 - - - +
200D GLY* 4.4 7.2 - - - +
201D SER 3.8 11.0 - - - +
202D LEU* 3.8 42.8 - - + +
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LYS* 4.6 8.1 - - - +
173D ILE 3.7 4.0 + - - -
174D TYR* 4.2 21.8 + - - -
180D ILE* 1.3 75.0 - - - +
182D LEU* 1.3 73.4 + - - +
196D VAL* 3.7 1.2 - - - +
197D GLU* 2.9 40.7 + - - +
198D ASN* 2.9 35.7 + - - +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 4.1 9.4 - - + -
139D LEU* 3.9 30.5 - - + -
141D ILE* 3.8 27.4 - - + -
156D LEU* 4.6 1.8 - - + -
172D LYS* 3.3 6.8 - - - +
173D ILE* 2.7 48.0 + - + +
175D VAL* 4.0 23.1 - - + -
180D ILE* 4.2 6.1 - - + -
181D SER* 1.3 86.6 + - - +
183D GLN* 1.3 59.9 + - - +
194D THR* 3.9 17.5 - - + +
195D GLU 3.5 3.8 - - - -
196D VAL* 4.0 18.8 - - + -
197D GLU* 4.5 1.6 - - - +
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Residues in contact with GLN 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLY* 3.9 34.3 + - - +
171D SER 3.6 2.7 - - - +
172D LYS* 4.4 17.9 - - + +
182D LEU* 1.3 74.1 - - - +
184D VAL* 1.3 67.3 + - - +
185D LYS* 3.4 24.5 + - - +
194D THR* 3.2 4.4 - - - -
195D GLU* 3.0 33.4 + - + +
197D GLU* 2.9 32.2 - - + +
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D VAL* 4.7 4.7 - - + -
168D GLU 3.9 18.6 - - - +
169D VAL* 3.4 22.7 - - + +
170D GLY* 3.0 23.7 + - - +
171D SER* 3.1 21.2 + - - +
173D ILE* 3.8 25.4 - - + -
183D GLN* 1.3 72.0 - - - +
185D LYS* 1.3 68.2 + - - +
186D GLN 3.4 20.6 - - - +
187D LYS* 4.8 0.7 - - + -
192D LEU* 4.1 19.1 - - + -
193D VAL 3.6 5.8 - - - +
194D THR* 4.1 4.7 - - + -
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Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.5 19.1 - - - +
183D GLN* 3.7 32.2 + - - +
184D VAL* 1.3 81.3 - - - +
186D GLN* 1.3 80.2 + - - +
193D VAL* 2.6 18.6 + - + +
194D THR 4.2 1.6 - - - -
195D GLU* 3.8 36.9 + - + +
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Residues in contact with GLN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.0 4.9 - - - -
184D VAL* 3.4 10.2 - - - +
185D LYS* 1.3 97.0 + - - +
187D LYS* 1.3 61.4 + - - +
188D GLY 4.3 0.7 - - - -
191D PHE* 6.3 1.3 - - + -
192D LEU* 3.5 1.0 - - - -
193D VAL* 2.9 51.0 + - + +
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Residues in contact with LYS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D CYS* 4.0 18.3 + - + +
167D VAL 3.4 22.2 + - - +
168D GLU* 3.7 18.1 + - - +
169D VAL* 4.1 14.3 - - + +
184D VAL* 4.8 0.9 - - + -
186D GLN* 1.3 78.4 - - - +
188D GLY* 1.3 70.9 + - - +
191D PHE* 3.8 2.7 - - - -
192D LEU* 3.7 21.1 - - + -
222E GLU* 3.4 43.4 - - + +
225E ILE* 3.4 33.3 - - - +
226E GLN* 4.8 5.5 - - - +
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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
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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