Contacts of the strand formed by residues 191 - 198 (chain A) in PDB entry 2AFW
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.4 37.2 - - + +
131A ALA* 4.6 2.4 - - - +
133A ARG* 3.2 33.7 - - + +
135A LEU 3.9 9.6 - - - +
181A LEU* 4.1 14.6 - - - +
189A PRO* 2.8 24.2 + - + +
190A ASP* 1.3 73.7 - - - +
192A SER* 1.3 71.2 + - - +
242A ASP* 3.8 18.2 - - - +
358A TYR* 3.8 18.2 - - + +
359A LEU* 3.9 18.0 - - + +
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Residues in contact with SER 192 (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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127A LEU* 3.2 24.0 + - - +
128A ASN* 2.7 35.6 + - - -
131A ALA* 4.4 2.0 - - - -
133A ARG 3.0 8.3 + - - -
134A HIS* 3.3 10.0 - - - -
135A LEU 2.9 23.9 + - - -
181A LEU* 3.5 10.9 - - - +
191A LEU* 1.3 76.5 - - - +
193A LEU* 1.3 66.0 + - - -
359A LEU* 3.6 15.5 - - - +
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Residues in contact with LEU 193 (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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102A TRP* 3.8 24.8 - - + -
126A THR 3.9 0.2 - - - -
127A LEU* 2.9 36.4 + - + +
134A HIS* 3.6 5.0 - - - -
135A LEU* 3.4 39.0 - - + +
137A LEU* 4.2 13.5 - - + -
170A LEU* 4.3 17.9 - - + -
178A LEU* 4.0 26.2 - - + -
181A LEU* 5.1 0.2 - - + -
192A SER* 1.3 84.5 + - - +
194A GLN* 1.3 67.0 + - - +
195A LEU* 4.6 2.7 - - + -
355A VAL* 4.2 11.2 - - + -
359A LEU* 4.0 9.4 - - + -
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Residues in contact with GLN 194 (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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102A TRP* 4.5 0.2 - - - -
105A GLU* 5.3 0.7 - - - +
124A ILE* 3.4 21.1 - - + +
125A SER 3.3 6.1 - - - +
126A THR* 2.9 31.5 + - - +
134A HIS* 4.2 14.3 - - + +
135A LEU 3.0 10.6 + - - +
136A VAL* 3.3 26.0 - - + +
137A LEU 3.0 24.3 + - - -
193A LEU* 1.3 77.3 - - - +
195A LEU* 1.3 71.5 + - - +
196A ILE* 3.9 15.0 - - + +
223A MET* 4.0 19.7 - - - +
241A MET* 5.3 0.6 - - - +
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Residues in contact with LEU 195 (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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95A ILE* 4.4 8.3 - - + -
102A TRP* 3.8 32.5 - - + -
123A ILE 3.9 0.3 - - - +
124A ILE* 3.5 3.6 - - - +
125A SER* 2.8 41.3 + - - +
137A LEU* 3.2 33.9 - - + -
167A MET* 3.8 32.1 - - + +
168A LEU* 5.7 0.4 - - + -
170A LEU* 5.1 2.2 - - + -
171A ALA* 4.5 6.3 - - + -
193A LEU* 4.6 6.3 - - + -
194A GLN* 1.3 80.9 - - - +
196A ILE* 1.3 63.8 + - - +
197A PHE* 3.9 23.0 - - + -
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Residues in contact with ILE 196 (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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122A ASN* 5.2 1.3 - - + -
123A ILE 3.5 7.4 - - - +
124A ILE* 4.2 11.0 - - + -
136A VAL* 3.5 26.9 - - + -
137A LEU 2.9 7.7 + - - -
138A ALA* 3.1 29.3 - - + +
139A CYS 3.1 6.9 + - - +
167A MET* 3.5 3.3 - - - +
194A GLN* 3.9 15.7 - - - +
195A LEU* 1.3 79.3 - - - +
197A PHE* 1.3 64.6 + - - +
198A PHE* 3.5 39.9 - - + -
219A LEU* 3.7 23.1 - - + -
223A MET* 4.7 10.3 - - + -
241A MET* 5.4 1.1 - - + -
244A LEU* 5.0 2.0 - - + -
310A PHE* 5.0 4.7 - - + -
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Residues in contact with PHE 197 (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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91A ILE* 3.7 40.2 - - + -
95A ILE* 4.0 10.5 - - + -
122A ASN* 3.6 1.0 - - - -
123A ILE* 2.8 53.3 + - + -
125A SER* 4.9 1.1 - - - -
139A CYS* 3.4 20.6 - - - -
141A TYR* 3.5 22.0 - - + +
164A CYS* 3.9 26.0 - - + -
167A MET* 3.7 24.7 - - + -
168A LEU* 4.2 14.8 - - + -
195A LEU* 3.9 24.2 - - + -
196A ILE* 1.3 74.6 - - - +
198A PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 198 (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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122A ASN* 3.4 10.8 - - - +
138A ALA* 3.7 22.9 - - + -
139A CYS 2.8 28.4 + - - +
140A HIS* 3.2 4.5 - - + +
141A TYR* 2.8 29.9 + - - -
142A ASP* 3.8 0.5 - - - +
196A ILE* 3.5 25.8 - - + -
197A PHE* 1.3 72.3 - - - +
199A ASP* 1.3 66.5 + - - +
215A GLY 3.9 1.1 - - - -
216A SER* 3.6 30.1 - - - +
219A LEU* 3.9 7.0 - - + -
244A LEU* 5.3 4.3 - - + -
246A LEU* 4.5 2.5 - - + -
306A ASP* 3.5 42.6 - - + +
310A PHE* 3.5 32.5 - + - -
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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