Contacts of the strand formed by residues 187 - 195 (chain A) in PDB entry 3AB0
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 SER 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE 3.9 0.2 - - - +
127A VAL* 3.6 2.9 - - - +
128A ILE* 2.7 45.9 + - - +
155A VAL* 4.1 3.8 - - - -
156A ASN* 3.3 19.6 + - - +
182A ILE* 3.4 39.3 - - - +
183A THR 5.1 0.2 + - - -
184A THR* 2.7 23.5 + - - -
186A PRO* 1.3 73.8 - - - +
188A LEU* 1.3 62.4 + - - +
189A VAL 4.1 0.2 - - - -
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Residues in contact with LEU 188 (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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125A THR* 4.2 10.5 - - + -
126A PHE 3.3 4.5 - - - +
127A VAL* 4.0 22.7 - - + -
154A GLN 3.1 6.1 - - - +
155A VAL* 3.4 1.4 - - - -
156A ASN* 2.7 42.8 + - - +
157A GLY 4.4 0.6 + - - +
186A PRO 4.7 7.2 - - - +
187A SER* 1.3 77.5 - - - +
189A VAL* 1.3 62.3 + - - +
190A GLU* 4.9 4.7 - - + +
101B TRP* 3.7 24.2 - - + +
91C TYR* 3.4 41.7 - - + +
92C HIS* 3.7 19.5 - - + +
94C TYR* 4.7 13.2 - - + +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 3.9 0.4 - - - -
126A PHE* 2.7 46.2 + - + +
128A ILE* 3.5 33.7 - - + -
136A ILE* 3.9 24.9 - - + -
153A ILE* 4.1 13.2 - - + -
154A GLN 3.8 2.5 - - - -
155A VAL* 4.1 14.6 - - + -
187A SER 4.0 0.6 + - - +
188A LEU* 1.3 74.8 - - - +
190A GLU* 1.3 65.3 - - - +
208A ILE* 4.6 9.0 - - + -
210A ILE* 3.8 26.2 - - + -
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Residues in contact with GLU 190 (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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104A PRO* 4.7 9.7 - - + +
124A ASP* 3.4 21.0 - - - +
125A THR* 3.4 28.6 + - + +
126A PHE* 5.0 2.5 - - - -
153A ILE* 4.3 0.2 - - - +
154A GLN* 2.8 44.6 + - + +
188A LEU* 4.9 4.0 - - + +
189A VAL* 1.3 78.4 - - - +
191A VAL* 1.3 65.9 + - - +
192A ILE* 3.9 22.2 - - + +
50C ARG* 5.0 4.3 + - - -
91C TYR* 3.8 10.8 + - - -
92C HIS* 2.8 36.8 + - + -
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Residues in contact with VAL 191 (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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104A PRO* 3.3 1.9 - - - +
105A VAL* 2.7 53.9 + - + +
107A PHE* 3.9 15.4 - - + -
124A ASP 4.9 1.6 + - - -
126A PHE* 5.8 0.2 - - + -
138A VAL* 3.9 28.9 - - + -
151A LEU* 4.3 15.7 - - + -
152A THR 3.3 18.2 - - - +
153A ILE* 4.7 6.3 - - + +
176A ILE* 4.7 3.8 - - + -
190A GLU* 1.3 74.0 - - - +
192A ILE* 1.3 60.5 + - - +
208A ILE* 3.9 27.8 - - + -
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Residues in contact with ILE 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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102A ASN* 3.4 38.4 - - - +
103A ASP 3.7 0.2 - - - -
104A PRO* 3.5 28.0 - - + -
151A LEU* 3.4 4.3 - - - -
152A THR* 2.8 38.8 + - + +
154A GLN* 3.3 49.1 - - + +
190A GLU* 4.1 19.1 - - - +
191A VAL* 1.3 72.9 - - - +
193A VAL* 1.3 76.2 + - - +
194A THR* 3.5 2.8 + - + -
32C TYR* 3.8 4.3 - - + +
50C ARG* 4.9 2.7 - - - +
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Residues in contact with VAL 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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99A LEU* 3.5 32.3 - - + -
100A GLY 3.8 12.3 - - - +
101A ILE* 4.5 0.8 - - - -
102A ASN* 3.1 23.0 + - - -
103A ASP 2.9 23.3 + - - +
105A VAL* 4.5 2.2 - - + -
150A GLY 3.5 7.6 - - - +
151A LEU* 3.7 15.3 - - + -
192A ILE* 1.3 78.9 - - - +
194A THR* 1.3 73.8 - - - +
197A GLY* 3.7 23.6 - - - -
198A LEU* 3.8 13.0 - - + +
70F SER* 4.4 1.9 + - - -
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Residues in contact with THR 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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101A ILE* 5.9 0.4 - - - +
149A GLY* 3.5 2.6 - - - -
150A GLY* 2.7 47.7 + - - +
151A LEU* 3.3 6.1 + - - -
152A THR* 3.9 15.9 - - + -
154A GLN* 5.5 0.7 - - - +
164A GLY* 5.6 1.6 - - - -
165A SER 4.9 1.0 + - - -
166A SER* 5.6 0.7 + - - -
192A ILE* 3.5 3.6 + - + +
193A VAL* 1.3 86.3 - - - +
195A GLY* 1.3 63.0 + - - +
25F SER* 4.7 5.3 - - - -
69F THR* 3.2 39.3 - - - +
70F SER* 3.7 17.3 - - - +
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Residues in contact with GLY 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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101A ILE* 3.3 18.9 - - - +
148A LEU 4.4 1.6 - - - -
149A GLY* 3.8 9.6 - - - -
150A GLY 4.0 1.1 - - - -
194A THR* 1.3 74.6 + - - +
196A LEU* 1.3 57.5 + - - -
197A GLY 2.9 12.4 + - - -
8F SER* 5.7 0.9 - - - -
23F SER* 3.2 25.4 + - - -
25F SER* 4.4 10.8 - - - -
70F SER* 4.0 9.4 - - - -
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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