Contacts of the strand formed by residues 138 - 148 (chain A) in PDB entry 1AF6
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 LYS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO 5.7 1.0 + - - -
97A GLY* 5.8 4.8 + - - -
131A ASN* 3.5 38.2 + - - +
132A ILE 3.4 3.8 - - - +
133A ASP* 4.0 36.3 + - - +
137A GLY* 1.3 78.5 - - - +
139A LEU* 1.3 60.9 + - - +
140A SER* 4.2 1.9 + - - +
175A ARG 3.6 1.2 - - - +
176A LEU* 3.2 5.6 - - - +
177A ALA* 2.8 46.9 + - + +
178A GLN* 3.3 30.5 - - + +
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Residues in contact with LEU 139 (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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131A ASN 3.2 3.5 + - - -
132A ILE* 2.7 67.5 + - + +
134A VAL* 4.5 20.4 - - + -
137A GLY 4.2 0.4 + - - -
138A LYS* 1.3 70.8 - - - +
140A SER* 1.3 63.8 + - - +
141A LEU* 4.5 13.9 - - + -
174A VAL* 3.9 23.1 - - + -
175A ARG 3.3 15.9 - - - +
176A LEU* 4.5 14.4 - - + -
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Residues in contact with SER 140 (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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107A TYR* 3.2 24.0 - - - -
108A GLN* 3.7 9.0 + - - -
129A LEU 3.6 4.7 - - - -
130A GLU* 3.7 8.9 - - - +
131A ASN* 3.0 24.3 + - - -
138A LYS* 5.1 2.1 - - - +
139A LEU* 1.3 74.6 + - - +
141A LEU* 1.3 64.0 + - - +
173A ASP* 3.8 1.4 - - - +
174A VAL* 3.4 4.9 - - - +
175A ARG* 2.9 42.8 + - - +
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Residues in contact with LEU 141 (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 TRP* 4.9 0.3 + - - -
107A TYR* 4.5 2.9 + - - -
128A GLY* 3.2 2.2 - - - -
129A LEU* 2.9 49.2 + - + +
132A ILE* 4.4 19.3 - - + -
139A LEU* 4.5 13.0 - - + -
140A SER* 1.3 79.9 - - - +
142A ALA* 1.3 61.8 + - - +
173A ASP 3.4 4.3 - - - +
174A VAL* 3.8 30.3 - - + -
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Residues in contact with ALA 142 (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 TRP* 4.0 11.9 - - + -
107A TYR* 3.9 32.3 - - + -
122A ILE* 4.5 4.3 - - + -
127A ALA 3.4 11.0 - - - +
128A GLY* 4.1 0.7 - - - -
141A LEU* 1.3 77.3 - - - +
143A ALA* 1.3 62.0 + - - +
144A THR* 5.0 0.4 - - + -
171A VAL 3.8 0.2 - - - +
172A PHE* 3.7 2.3 - - - +
173A ASP* 2.8 40.9 + - + +
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Residues in contact with ALA 143 (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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126A GLY* 3.1 3.3 - - - -
127A ALA* 3.0 34.0 + - + +
142A ALA* 1.3 75.8 - - - +
144A THR* 1.3 62.7 + - - +
171A VAL 3.3 10.3 - - - +
172A PHE* 4.0 18.2 - - + -
11B ILE* 4.0 3.9 - - + +
13B TRP* 4.2 24.0 - - + -
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Residues in contact with THR 144 (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 TRP* 4.5 13.2 - - + -
105A ARG 5.9 0.2 - - - +
107A TYR* 5.1 3.4 - - + -
122A ILE* 2.8 54.1 + - + +
123A SER* 5.1 0.7 - - - -
124A GLY 4.6 7.9 - - - +
125A PRO 3.2 14.4 - - - +
126A GLY* 4.2 4.9 - - - -
142A ALA* 4.3 1.3 - - + -
143A ALA* 1.3 80.8 - - - +
145A ARG* 1.3 62.5 + - - +
170A ASP* 3.8 3.6 - - - +
171A VAL* 3.1 37.6 + - - +
246A LEU* 4.3 4.3 - - - +
11B ILE* 3.9 5.5 - - - +
13B TRP* 6.0 0.2 - - - -
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Residues in contact with ARG 145 (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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123A SER 4.8 3.1 - - - +
124A GLY* 4.3 4.7 - - - -
125A PRO* 3.0 32.5 + - + +
144A THR* 1.3 77.1 + - - +
146A SER* 1.3 79.8 + - - +
168A ALA* 4.0 12.5 - - - +
169A ASN 3.7 5.4 - - - -
170A ASP* 2.9 26.6 + - - -
197A ASN* 5.0 0.6 - - - +
246A LEU* 5.1 2.9 - - - +
11B ILE* 3.8 21.7 - - + +
12B GLY 3.0 30.5 + - - +
13B TRP* 3.3 20.4 - - - +
19B GLU* 3.4 16.4 - - - +
20B GLN* 4.6 0.4 - - - +
70B GLN 4.3 3.4 + - - +
71B GLN* 3.1 52.8 + - - +
72B ASN* 4.3 1.6 - - - -
73B ASP 5.0 0.2 + - - -
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Residues in contact with SER 146 (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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144A THR 4.4 0.2 + - - -
145A ARG* 1.3 80.4 - - - +
147A SER* 1.3 62.6 + - - +
148A GLU* 6.2 0.2 - - - +
169A ASN* 2.8 32.4 + - - +
171A VAL* 5.7 1.0 - - - +
246A LEU* 4.1 33.0 - - - +
247A SER 3.7 20.1 + - - -
248A GLN* 5.9 0.2 - - - +
71B GLN 3.1 11.2 - - - -
72B ASN* 3.4 9.6 - - - -
73B ASP 6.1 0.2 - - - -
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Residues in contact with SER 147 (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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146A SER* 1.3 79.3 - - - +
148A GLU* 1.3 62.4 + - - +
149A ALA 4.0 0.3 + - - -
166A GLU* 2.6 36.7 + - - -
167A THR 3.4 10.5 - - - -
168A ALA* 4.2 6.1 - - - -
169A ASN* 4.3 0.9 - - - +
19B GLU* 5.6 0.9 - - - -
71B GLN* 3.8 16.1 - - - +
72B ASN* 2.9 32.0 + - - +
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Residues in contact with GLU 148 (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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147A SER* 1.3 74.8 - - - +
149A ALA* 1.3 66.0 + - - +
150A GLY 3.2 11.7 - - - +
166A GLU* 3.1 20.2 - - - +
167A THR* 2.9 20.2 + - - +
169A ASN* 2.8 23.9 - - - +
247A SER 4.9 0.2 - - - +
248A GLN* 3.6 33.3 - - + +
249A GLY 3.2 1.7 + - - -
250A SER* 2.5 51.4 + - - +
251A GLY* 3.6 4.0 + - - -
252A VAL 4.5 7.7 + - - +
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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