Contacts of the strand formed by residues 208 - 215 (chain A) in PDB entry 1H1B
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 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLN* 3.7 31.9 - - + +
123A LEU 3.6 15.3 - - - +
124A PRO* 3.4 35.2 - - + -
128A ARG* 3.2 31.2 - - - +
200A VAL* 3.6 0.3 - - - -
201A CYS 3.0 26.8 + - - -
204A ASN 4.0 8.7 - - - +
205A GLY* 1.3 78.8 - - - +
209A ILE* 1.3 63.1 + - - +
210A HIS* 3.1 19.5 + - + +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.1 11.7 - - + -
45A THR* 4.3 10.3 - - + +
53A MET* 4.4 7.4 - - + -
121A ALA* 3.9 18.8 - - + -
122A GLN 3.3 14.7 + - - +
123A LEU* 3.9 13.2 - - + -
124A PRO* 3.3 19.5 - - - +
198A PRO* 3.8 20.2 - - + -
199A LEU 3.7 2.5 - - - +
200A VAL* 3.5 32.5 - - + -
205A GLY 5.2 1.3 - - - +
208A LEU* 1.3 72.1 - - - +
210A HIS* 1.3 59.6 + - - +
211A GLY 3.7 21.3 - - - +
212A ILE* 5.3 0.7 - - + -
231A VAL* 3.3 19.9 - - + +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.8 12.6 - - + +
128A ARG* 3.4 50.1 + - - -
130A LEU* 3.4 35.5 - - + +
181A VAL* 3.9 12.2 - - + +
199A LEU* 3.0 8.2 + - + -
201A CYS* 3.5 28.1 + - + -
208A LEU* 3.1 46.7 + - + +
209A ILE* 1.3 73.5 - - - +
211A GLY* 1.3 57.7 + - - +
229A ALA 3.6 1.6 - - - +
230A PRO* 3.8 4.2 - - - +
231A VAL* 3.2 22.9 + - - -
232A ALA* 4.6 4.3 + - - +
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Residues in contact with GLY 211 (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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181A VAL* 5.3 0.9 - - - -
198A PRO* 3.5 5.4 - - - +
199A LEU* 2.9 39.5 + - - +
209A ILE* 3.4 5.4 - - - +
210A HIS* 1.3 81.0 - - - +
212A ILE* 1.3 67.8 + - - +
228A PHE* 3.8 9.6 - - - -
229A ALA 3.2 9.2 - - - -
231A VAL* 3.6 2.6 - - - +
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Residues in contact with ILE 212 (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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45A THR* 5.8 1.6 - - - +
53A MET* 3.5 42.4 - - + +
54A SER 3.6 3.1 - - - +
55A ALA* 3.6 30.1 - - + +
102A ASP 4.3 2.0 - - - +
103A ILE* 3.6 27.8 - - + -
196A GLY* 3.6 18.8 - - - +
197A SER 3.3 3.8 - - - +
198A PRO* 5.4 1.6 - - + -
209A ILE* 5.3 1.3 - - + -
211A GLY* 1.3 77.8 - - - +
213A ALA* 1.3 71.1 + - - +
214A SER* 3.1 1.9 + - - -
228A PHE* 3.2 3.4 - - - +
229A ALA* 3.0 33.6 + - + +
231A VAL* 3.9 11.4 - - + -
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Residues in contact with ALA 213 (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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55A ALA* 3.9 6.8 - - - +
190A VAL* 4.7 13.5 - - + -
194A ASP 3.5 26.0 - - - +
195A SER* 3.5 7.4 + - - -
196A GLY* 2.8 25.1 + - - -
197A SER* 2.7 19.4 + - - +
212A ILE* 1.3 72.1 - - - +
214A SER* 1.3 59.6 + - - +
227A ALA 4.3 0.4 - - - -
228A PHE* 3.4 24.7 - - + -
400A 151 4.5 4.9 - - + -
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Residues in contact with SER 214 (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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55A ALA* 5.1 0.2 - - - -
99A LEU* 4.0 4.9 - - - +
102A ASP* 2.6 40.9 + - - +
180A ASN* 5.1 1.5 + - - -
190A VAL* 6.0 0.4 - - - +
195A SER* 3.3 3.3 + - - -
212A ILE 3.8 7.0 - - - -
213A ALA* 1.3 75.4 - - - +
215A PHE* 1.4 77.5 + - - +
227A ALA 2.9 20.3 + - - -
228A PHE 4.5 0.7 - - - -
229A ALA* 4.2 8.5 - - - -
400A 151 3.3 29.8 - - - +
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Residues in contact with PHE 215 (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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99A LEU* 3.8 15.0 - + - +
177A ARG* 3.9 31.2 - - - -
180A ASN* 3.6 23.3 - - - -
182A CYS* 6.1 0.2 - - - -
190A VAL* 5.1 0.3 - - - +
214A SER* 1.4 99.5 - - - +
216A VAL* 1.3 73.8 + - - +
217A ARG* 3.4 32.3 - - + -
226A ASP* 3.9 0.9 - - - +
227A ALA* 2.9 54.7 + - + +
400A 151 3.5 46.0 - - + +
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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