Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 6IAP
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 TYR 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.7 6.7 - - + +
118A PHE* 3.6 47.1 - + + -
131A LEU* 3.7 24.2 - - + -
132A LEU 3.3 10.8 - - - +
133A LYS* 4.0 24.2 + - + +
141A GLN* 4.5 7.9 - - - -
153A LEU* 4.4 8.7 - - + +
160A HIS* 2.9 41.8 + - - +
161A ARG 3.9 5.4 + - - -
162A GLY* 3.2 25.6 - - - -
163A THR* 1.3 75.8 + - - +
165A ARG* 1.4 62.2 + - - +
181A PRO* 3.4 7.8 - - - +
182A VAL* 3.1 28.4 + - + -
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Residues in contact with ARG 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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102A LEU* 3.9 6.3 - - - -
130A LEU 3.9 0.3 - - - +
131A LEU* 3.6 5.1 - - - +
132A LEU* 2.8 51.7 + - + +
134A GLU* 2.8 42.2 + - + -
164A TYR* 1.4 77.4 - - - +
166A CYS* 1.3 60.4 + - - +
167A PHE* 4.9 7.2 - - + -
178A PRO* 3.6 29.6 - - + +
179A SER 3.3 20.7 + - - +
180A GLU* 5.3 0.2 - - - +
181A PRO* 3.5 35.8 - - + +
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Residues in contact with CYS 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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100A PRO* 3.7 3.2 - - - +
102A LEU* 3.8 15.2 - - + +
120A CYS* 2.0 50.9 - - - -
129A PHE* 4.3 2.7 - - - -
130A LEU 3.3 13.7 - - - +
131A LEU* 4.9 2.7 - - + -
151A PHE* 4.6 4.0 - - - -
165A ARG* 1.3 76.4 - - - +
167A PHE* 1.3 75.3 + - - +
178A PRO* 3.6 2.3 - - - +
179A SER* 2.8 47.8 + - - +
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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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14A MET* 4.5 6.1 - - - -
94A THR* 3.8 21.3 - - + -
100A PRO* 4.1 0.4 - - - -
129A PHE* 3.5 1.7 - - - -
130A LEU* 2.8 43.0 + - + +
132A LEU* 4.4 34.5 - - + -
165A ARG* 4.9 5.6 - - + -
166A CYS* 1.3 85.1 - - - +
168A GLY* 1.3 64.4 + - - +
175A TRP* 3.8 32.1 - + + -
176A SER* 3.2 27.4 - - - -
177A PHE 3.9 4.0 - - - -
178A PRO* 3.7 33.4 - - + -
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Residues in contact with GLY 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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100A PRO* 3.6 3.6 - - - +
122A LEU* 4.3 12.8 - - - -
125A ALA* 5.1 0.4 - - - -
128A MET 4.2 1.3 - - - -
129A PHE* 4.1 19.3 - - - -
130A LEU* 5.1 0.7 - - - -
167A PHE* 1.3 76.7 - - - +
169A SER* 1.3 56.0 + - - -
175A TRP* 3.3 6.9 - - - +
176A SER* 2.7 43.9 + - - -
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Residues in contact with SER 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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125A ALA* 3.8 6.6 - - - +
126A THR* 2.7 52.8 + - - -
128A MET* 3.0 41.5 + - - +
130A LEU* 4.4 1.6 - - - -
168A GLY* 1.3 74.3 - - - -
170A TYR* 1.3 63.3 + - - +
171A ASN 3.5 18.5 + - - -
174A ALA 3.5 4.0 - - - -
175A TRP* 3.9 9.4 - - - +
176A SER 4.5 0.2 - - - +
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Residues in contact with TYR 170 (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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96A MET* 3.9 8.7 - - + -
97A TYR* 3.5 42.6 - + + -
98A ASP* 2.6 38.4 + - - +
122A LEU* 3.8 10.1 - - + +
124A THR 3.2 24.7 - - - -
125A ALA* 4.0 9.0 - - + -
126A THR* 3.9 15.5 - - - +
169A SER* 1.3 76.8 - - - +
171A ASN* 1.3 66.9 + - - +
174A ALA* 2.7 23.0 + - + +
176A SER* 3.6 27.3 - - - -
52H TYR* 4.3 7.0 - + - -
55H SER* 5.6 6.8 - - - -
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Residues in contact with ASN 171 (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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66A SER* 5.5 4.8 + - - -
69A ALA* 5.5 0.9 - - - +
126A THR* 4.3 4.9 - - - +
169A SER* 3.5 16.1 + - - -
170A TYR* 1.3 80.1 + - - +
172A ASN* 1.3 55.3 + - - +
173A HIS* 2.8 24.1 + - - +
174A ALA* 2.8 56.0 + - - +
175A TRP* 3.9 0.2 - - - -
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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