Contacts of the strand formed by residues 138 - 148 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PRO 5.7 1.6 + - - -
97C GLY* 5.8 4.0 + - - -
131C ASN* 3.6 36.4 + - - +
132C ILE 3.4 9.4 - - - +
133C ASP* 4.1 29.4 + - - +
137C GLY* 1.3 80.5 - - - +
139C LEU* 1.3 60.7 + - - +
140C SER* 5.2 1.7 + - - +
175C ARG 3.6 1.0 - - - +
176C LEU* 3.3 5.6 - - - -
177C ALA* 2.7 48.0 + - + +
178C GLN* 3.3 29.8 - - + +
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ASN 3.3 3.3 + - - -
132C ILE* 2.7 64.8 + - + +
134C VAL* 4.5 23.6 - - + -
137C GLY 4.1 0.6 + - - -
138C LYS* 1.3 73.2 - - - +
140C SER* 1.3 63.4 + - - +
141C LEU* 4.5 12.8 - - + -
174C VAL* 3.9 22.9 - - + -
175C ARG 3.3 15.7 - - - +
176C LEU* 4.5 12.8 - - + -
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TYR* 3.3 22.2 - - - -
108C GLN* 3.7 9.3 + - - -
129C LEU 3.6 4.0 - - - -
130C GLU* 3.6 9.2 - - - +
131C ASN* 3.0 25.0 + - - -
138C LYS* 5.2 2.3 - - - +
139C LEU* 1.3 74.2 + - - +
141C LEU* 1.3 64.7 + - - +
173C ASP* 3.8 0.9 - - - +
174C VAL* 3.4 5.5 - - - +
175C ARG* 2.9 42.9 + - - +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 4.9 0.3 + - - -
107C TYR* 4.5 2.5 + - - -
128C GLY* 3.2 2.0 - - - -
129C LEU* 2.9 47.4 + - + +
132C ILE* 4.5 19.1 - - + -
139C LEU* 4.5 12.6 - - + -
140C SER* 1.3 82.4 - - - +
142C ALA* 1.3 62.6 + - - +
173C ASP* 3.4 3.8 - - - +
174C VAL* 3.8 31.0 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 4.0 12.3 - - + -
107C TYR* 3.9 32.3 - - + -
122C ILE* 4.6 4.3 - - + -
127C ALA 3.5 11.2 - - - +
128C GLY* 4.1 0.9 - - - -
141C LEU* 1.3 76.7 - - - +
143C ALA* 1.3 60.9 + - - +
144C THR* 5.0 0.4 - - + -
172C PHE* 3.7 2.6 - - - +
173C ASP* 2.8 43.0 + - + +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.0 4.1 - - + +
13A TRP* 4.2 23.6 - - + -
126C GLY* 3.1 3.6 - - - -
127C ALA* 3.0 32.9 + - + +
142C ALA* 1.3 74.4 - - - +
144C THR* 1.3 63.1 + - - +
171C VAL 3.3 9.9 - - - +
172C PHE* 4.0 18.4 - - + -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 5.3 - - - +
13A TRP* 5.9 0.2 - - - -
101C TRP* 4.5 13.9 - - + -
105C ARG 6.0 0.2 - - - +
107C TYR* 5.2 2.7 - - + -
122C ILE* 2.7 55.6 + - + +
123C SER* 5.1 0.4 - - - -
124C GLY 4.7 7.2 - - - +
125C PRO 3.2 13.2 - - - +
126C GLY* 4.3 4.5 - - - -
142C ALA* 5.0 1.1 - - + -
143C ALA* 1.3 81.2 - - - +
145C ARG* 1.3 62.5 + - - +
170C ASP* 3.8 3.8 - - - +
171C VAL* 3.1 37.3 + - - +
246C LEU* 4.3 4.0 - - - +
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Residues in contact with ARG 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 22.0 - - + +
12A GLY 2.9 30.5 + - - +
13A TRP* 3.4 20.6 - - - +
19A GLU* 3.4 15.2 - - - +
20A GLN 4.6 0.2 - - - +
70A GLN 4.2 2.8 + - - +
71A GLN* 3.0 53.5 + - - +
72A ASN* 4.3 1.6 - - - -
73A ASP 5.0 0.2 + - - -
123C SER 4.7 2.4 - - - +
124C GLY* 4.3 4.7 - - - -
125C PRO* 2.9 33.3 + - + +
144C THR* 1.3 76.9 + - - +
146C SER* 1.3 78.8 + - - +
168C ALA* 4.0 11.9 - - - +
169C ASN 3.6 4.9 - - - -
170C ASP* 2.9 25.5 + - - -
197C ASN* 5.1 0.8 - - - +
246C LEU* 5.1 3.5 - - - +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLN 3.1 12.1 - - - -
72A ASN* 3.4 10.5 - - - -
73A ASP 6.0 0.2 - - - -
145C ARG* 1.3 80.2 - - - +
147C SER* 1.3 62.8 + - - +
169C ASN* 2.8 33.2 + - - +
171C VAL* 5.8 0.9 - - - +
246C LEU* 4.2 32.6 - - - +
247C SER 3.7 20.1 + - - -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 5.6 0.4 - - - -
71A GLN* 3.7 18.6 - - - +
72A ASN* 3.0 29.8 + - - +
146C SER* 1.3 79.7 - - - +
148C GLU* 1.3 62.5 + - - +
149C ALA 3.9 0.9 + - - -
166C GLU* 2.6 38.5 + - - -
167C THR 3.3 8.1 - - - -
168C ALA* 4.2 6.5 - - - -
169C ASN* 4.3 0.4 - - - +
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C SER* 1.3 75.0 - - - +
149C ALA* 1.3 64.5 + - - +
150C GLY 3.8 11.9 - - - +
166C GLU* 3.0 20.7 - - - +
167C THR* 2.9 20.6 + - - +
169C ASN* 2.8 23.9 - - - +
247C SER 4.9 0.7 - - - +
248C GLN* 3.6 32.6 - - + +
249C GLY 3.3 0.9 + - - -
250C SER* 2.7 51.0 + - - +
251C GLY* 3.6 4.0 + - - -
252C VAL 4.6 7.6 + - - +
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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