Contacts of the strand formed by residues 138 - 148 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B GLY* 5.7 5.1 + - - -
131B ASN* 3.6 37.2 + - - +
132B ILE 3.4 2.9 - - - +
133B ASP* 4.1 34.7 + - - +
137B GLY* 1.3 79.2 - - - +
139B LEU* 1.3 61.0 + - - +
140B SER* 4.2 2.3 + - - +
175B ARG 3.6 1.4 - - - +
176B LEU* 3.3 5.9 - - - +
177B ALA* 2.8 46.0 + - + +
178B GLN* 3.3 30.5 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ASN 3.3 2.3 + - - -
132B ILE* 2.7 66.1 + - + +
134B VAL* 4.5 18.8 - - + -
137B GLY 4.2 0.8 + - - -
138B LYS* 1.3 72.3 - - - +
140B SER* 1.3 63.0 + - - +
141B LEU* 4.4 15.5 - - + -
174B VAL* 3.8 23.6 - - + -
175B ARG 3.3 15.7 - - - +
176B LEU* 4.4 17.0 - - + -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.2 22.4 - - - -
108B GLN* 3.7 9.0 + - - -
129B LEU 3.6 5.4 - - - -
130B GLU* 3.6 9.2 - - - +
131B ASN* 3.0 24.7 + - - -
138B LYS* 5.1 2.3 - - - +
139B LEU* 1.3 72.8 - - - +
141B LEU* 1.3 63.7 + - - +
173B ASP* 4.5 0.8 - - - -
174B VAL* 3.4 5.4 - - - +
175B ARG* 2.9 43.6 + - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 5.0 0.3 + - - -
107B TYR* 4.5 2.9 + - - -
128B GLY* 3.2 2.9 - - - -
129B LEU* 2.9 49.1 + - + +
132B ILE* 4.4 20.0 - - + -
139B LEU* 4.4 12.8 - - + -
140B SER* 1.3 80.6 - - - +
142B ALA* 1.3 60.2 + - - +
173B ASP 3.4 4.3 - - - +
174B VAL* 3.8 31.0 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 4.0 11.2 - - + -
107B TYR* 3.9 32.5 - - + -
122B ILE* 4.4 4.7 - - + -
127B ALA 3.4 11.2 - - - +
128B GLY* 4.1 0.7 - - - -
141B LEU* 1.3 75.4 - - - +
143B ALA* 1.3 62.4 + - - +
144B THR* 4.4 0.7 - - + -
172B PHE* 3.7 2.4 - - - +
173B ASP* 2.8 42.6 + - + +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY* 3.1 2.8 - - - -
127B ALA* 3.0 33.1 + - + +
142B ALA* 1.3 74.5 - - - +
144B THR* 1.3 62.1 + - - +
171B VAL 3.3 10.5 - - - +
172B PHE* 4.1 17.3 - - + -
11C ILE* 4.0 4.8 - - + +
13C TRP* 4.2 24.7 - - + -
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 4.5 13.2 - - + -
105B ARG 5.8 0.4 - - - +
107B TYR* 5.2 2.9 - - + -
122B ILE* 2.8 53.5 + - + +
123B SER* 5.1 0.7 - - - -
124B GLY 4.6 8.5 - - - +
125B PRO 3.2 13.0 - - - +
126B GLY* 4.2 5.4 - - - -
142B ALA* 5.0 0.9 - - + -
143B ALA* 1.3 81.0 - - - +
145B ARG* 1.3 62.8 + - - +
170B ASP* 3.8 4.2 - - - +
171B VAL* 3.1 36.7 + - - +
246B LEU* 4.3 4.2 - - - +
11C ILE* 4.0 4.8 - - - +
13C TRP* 6.0 0.3 - - - -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 4.8 2.1 - - - +
124B GLY* 4.3 4.9 - - - -
125B PRO* 3.0 30.3 + - + +
144B THR* 1.3 78.0 - - - +
146B SER* 1.3 79.9 + - - +
168B ALA* 4.0 12.1 - - - +
169B ASN 3.6 5.2 - - - -
170B ASP* 2.9 25.5 + - - -
197B ASN* 5.0 0.6 - - - +
246B LEU* 5.0 3.0 - - - +
11C ILE* 3.8 20.9 - - + +
12C GLY 3.0 31.1 + - - +
13C TRP* 3.3 21.2 - - - +
19C GLU* 3.4 16.0 - - - +
20C GLN 4.6 0.2 - - - +
70C GLN 4.3 3.7 + - - +
71C GLN* 3.1 51.8 + - - +
72C ASN* 4.3 1.7 - - - -
73C ASP 5.0 0.2 + - - -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG* 1.3 81.3 - - - +
147B SER* 1.3 62.6 + - - +
169B ASN* 2.8 32.4 + - - +
171B VAL* 5.7 0.9 - - - +
246B LEU* 4.1 34.0 - - - +
247B SER 3.7 20.3 + - - -
71C GLN 3.1 11.7 - - - -
72C ASN* 3.5 10.5 - - - -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B SER* 1.3 79.4 - - - +
148B GLU* 1.3 62.5 + - - +
149B ALA 3.9 0.5 + - - -
166B GLU* 2.6 38.9 + - - -
167B THR 3.3 7.9 - - - -
168B ALA* 4.2 6.3 - - - -
169B ASN* 4.3 0.9 - - - +
19C GLU* 5.6 0.9 - - - -
71C GLN* 3.7 17.8 - - - +
72C ASN* 3.0 29.8 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER* 1.3 75.9 - - - +
149B ALA* 1.3 62.8 + - - +
150B GLY 3.3 12.1 - - - +
166B GLU* 3.0 23.0 - - - +
167B THR* 2.8 19.9 + - - +
169B ASN* 2.8 24.0 + - - +
247B SER 4.9 0.7 - - - +
248B GLN* 3.6 32.5 - - + +
249B GLY 3.3 1.6 + - - -
250B SER* 2.6 49.4 + - - +
251B GLY* 3.6 5.4 + - - -
252B VAL 4.5 8.7 + - - +
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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