Contacts of the strand formed by residues 126 - 140 (chain F) in PDB entry 6AHU
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 LEU 126 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F GLU 4.1 0.9 - - - +
105F VAL* 3.4 5.8 - - - -
106F TRP* 3.1 62.6 + - + +
108F SER* 3.9 31.4 - - - +
124F ALA* 4.7 5.8 - - + +
125F SER* 1.3 79.7 - - - +
127F SER* 1.3 61.4 + - - +
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ARG* 3.2 30.6 + - - -
104F GLU 3.9 4.5 - - - -
105F VAL* 4.0 17.5 - - - -
125F SER 4.2 1.0 + - - -
126F LEU* 1.3 74.5 - - - +
128F VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A C 5.7 9.9 - - - -
63A C 5.9 1.3 - - - +
102F VAL 4.0 0.5 - - - +
103F ARG* 3.5 10.4 - - - +
104F GLU* 3.4 47.4 + - + +
106F TRP* 4.4 16.8 - - - +
127F SER* 1.3 77.2 - - - +
129F LEU* 1.3 70.6 + - - +
130F LYS* 4.8 9.1 - - + +
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A C 3.8 14.6 + - - -
8F ARG* 5.4 4.5 - - - +
101F SER* 4.2 19.3 - - - -
102F VAL 3.8 11.7 - - - +
103F ARG* 4.0 31.5 - - + +
128F VAL* 1.3 80.6 - - - +
130F LYS* 1.3 70.8 + - - +
131F ASN* 4.6 17.0 + - - +
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Residues in contact with LYS 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A C 5.4 10.7 - - - +
61A C 5.3 1.2 + - - -
62A C 3.4 30.1 + - - +
63A C 4.8 4.5 - - - +
101F SER* 3.5 3.8 - - - -
102F VAL* 2.7 55.6 + - + +
104F GLU* 3.4 37.4 + - + +
128F VAL* 4.8 11.9 - - + +
129F LEU* 1.3 80.0 - - - +
131F ASN* 1.3 63.7 + - - +
132F VAL* 3.7 19.8 + - + +
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Residues in contact with ASN 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A C 5.1 6.7 + - - -
64A A 5.4 5.7 + - - +
8F ARG* 3.9 26.4 + - - +
99F TYR* 5.6 13.7 - - + -
100F ARG 3.8 4.7 - - - +
101F SER* 4.0 7.3 + - - -
129F LEU* 4.6 14.1 + - - +
130F LYS* 1.3 76.9 - - - +
132F VAL* 1.3 66.0 + - - +
133F PRO* 4.0 2.8 - - - +
83G ASN* 5.6 1.4 - - - +
87G GLN* 5.9 1.2 + - - -
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F CYS* 4.2 22.7 - - + -
71F GLY* 4.2 18.2 - - - +
99F TYR* 4.2 3.5 - - - -
100F ARG* 3.2 33.9 + - + +
102F VAL* 3.7 22.2 - - + -
130F LYS* 3.7 29.4 - - + +
131F ASN* 1.3 76.8 - - - +
133F PRO* 1.3 72.1 - - + +
86G LEU* 5.1 0.2 - - - +
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Residues in contact with PRO 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F CYS* 3.5 21.0 - - - +
71F GLY* 3.5 8.3 + - - +
74F THR* 4.7 6.9 - - + -
131F ASN 4.2 3.4 - - - +
132F VAL* 1.3 88.4 - - + +
134F GLY* 1.3 58.5 + - - +
79G ASN 4.8 3.8 - - - +
82G ILE* 3.7 40.2 - - + +
83G ASN* 4.5 23.1 - - + +
86G LEU* 3.8 24.2 - - + -
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Residues in contact with GLY 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F GLY 3.6 8.5 - - - -
74F THR* 4.7 0.4 - - - -
96F ARG 4.4 1.6 - - - -
97F LEU* 3.6 17.3 - - - +
98F ARG* 3.1 22.0 + - - -
100F ARG* 3.9 18.2 - - - -
132F VAL 3.8 0.2 + - - -
133F PRO* 1.3 75.1 - - - +
135F LEU* 1.3 63.1 + - - +
82G ILE* 3.5 13.0 - - - +
86G LEU* 4.2 0.7 - - - +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F SER* 3.5 1.0 - - - -
69F GLY 2.9 32.9 + - - +
74F THR* 3.4 24.5 - - - +
77F THR* 3.8 20.2 - - + -
78F VAL* 4.0 13.0 - - + -
95F THR* 3.8 13.9 - - + -
96F ARG 3.5 7.0 - - - +
97F LEU* 5.0 1.8 - - + -
100F ARG* 3.5 6.6 + - - -
134F GLY* 1.3 75.2 - - - +
136F ALA* 1.3 68.1 + - - +
137F ILE* 3.7 29.2 - - + -
82G ILE* 3.8 13.7 - - + -
130G ILE* 3.9 26.5 - - + -
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLY* 5.6 7.9 - - - +
66F VAL* 5.9 0.7 - - + -
67F PHE* 3.3 20.4 - - - +
68F SER* 5.1 0.2 - - - -
77F THR* 5.9 0.2 - - - -
94F VAL 3.0 14.6 - - - +
95F THR* 3.3 2.1 - - - -
96F ARG* 3.2 28.7 + - + +
100F ARG* 4.2 10.5 - - - +
135F LEU* 1.3 78.8 - - - +
137F ILE* 1.3 63.2 + - - +
138F LEU* 5.0 7.8 - - + +
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE 3.4 0.7 - - - +
67F PHE* 2.9 47.6 + - + +
77F THR* 3.7 24.7 - - - +
78F VAL* 4.1 11.9 - - + +
81F ALA* 3.8 18.6 - - + -
93F GLN* 3.6 32.8 - - + +
94F VAL 3.5 2.7 - - - -
95F THR* 3.8 14.6 - - - +
135F LEU* 3.7 21.5 - - + -
136F ALA* 1.3 75.8 - - - +
138F LEU* 1.3 63.3 + - - +
139F LEU* 4.3 6.1 - - + -
102G THR* 4.8 10.3 - - + +
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLY* 5.5 6.7 - - - -
24F GLY 6.1 0.4 - - - -
25F SER* 6.5 0.2 - - - -
28F PHE* 4.0 38.1 - - + -
65F ILE 3.5 2.9 - - - +
66F VAL* 3.8 41.5 - - + -
67F PHE 4.7 0.9 - - - +
92F HIS 3.6 0.5 - - - +
93F GLN* 3.4 4.6 - - - -
94F VAL* 3.1 48.7 + - + +
96F ARG* 4.6 22.9 - - + +
136F ALA* 5.0 6.7 - - + +
137F ILE* 1.3 77.5 - - - +
139F LEU* 1.3 64.5 + - - +
140F SER* 3.3 6.1 + - - -
144F LEU* 5.5 0.9 - - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PHE* 5.8 0.2 - - - -
63F ARG 3.8 1.0 - - - +
64F ALA* 3.4 4.9 + - - -
65F ILE* 3.1 38.1 + - + +
67F PHE* 3.6 27.4 - - + -
81F ALA* 4.3 15.7 - - + +
84F LEU* 3.8 25.4 - - + -
85F LYS* 5.4 9.4 - - + +
88F LEU* 5.4 9.0 - - + -
90F GLY* 5.1 16.4 - - - +
92F HIS 3.6 4.7 - - - +
93F GLN* 3.6 33.4 - - + +
137F ILE* 3.8 4.7 - - + -
138F LEU* 1.3 71.8 - - - +
140F SER* 1.3 60.7 + - - +
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Residues in contact with SER 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PHE* 4.7 13.9 - - - -
63F ARG* 3.1 21.4 + - - -
90F GLY* 5.1 2.9 - - - -
91F LEU 4.3 2.4 + - - -
92F HIS* 2.9 35.1 + - - +
138F LEU 3.3 4.4 + - - -
139F LEU* 1.3 73.5 - - - +
141F LYS* 1.3 69.6 + - - +
142F ASP 3.9 0.2 + - - -
143F ALA* 3.8 22.5 + - - +
144F LEU* 3.7 23.8 - - - +
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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