Contacts of the strand formed by residues 127 - 136 (chain B) in PDB entry 3C9T
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 GLY 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ASN* 5.7 0.2 - - - -
44B VAL* 5.1 0.9 - - - -
46B ASN* 3.7 17.5 - - - -
85B SER 3.7 0.6 - - - +
86B LEU* 3.3 8.3 - - - +
87B ASN* 2.8 47.8 + - - +
125B LYS 3.4 1.8 + - - -
126B ILE* 1.3 74.5 - - - +
128B ILE* 1.3 64.8 + - - +
129B SER* 4.1 1.1 - - - -
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Residues in contact with ILE 128 (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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43B ASP 3.6 1.4 - - - +
44B VAL* 3.1 7.4 - - - +
45B LEU* 2.9 46.7 + - + +
51B PHE* 4.1 14.4 - - + -
60B VAL* 3.6 22.9 - - + -
64B ALA* 3.8 17.5 - - + -
84B ILE* 4.3 7.2 - - + -
85B SER 3.8 1.8 - - - -
86B LEU* 3.8 14.6 - - + -
96B TYR* 4.9 2.2 - - + +
100B PHE* 3.5 41.3 - - + -
126B ILE* 4.1 12.8 - - + -
127B GLY* 1.3 76.6 - - - +
129B SER* 1.3 62.3 + - - +
130B VAL* 4.1 2.6 + - + +
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Residues in contact with SER 129 (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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85A SER* 3.4 12.0 + - - -
87A ASN* 5.2 3.3 + - - -
129A SER* 3.8 24.7 - - - -
42B THR* 5.1 0.4 - - - -
43B ASP 3.4 4.3 - - - -
44B VAL* 3.3 25.8 - - - +
83B LEU 4.0 0.3 - - - +
84B ILE* 3.4 2.4 - - - +
85B SER* 2.5 49.1 + - - -
127B GLY 4.1 0.5 - - - -
128B ILE* 1.3 70.9 + - - +
130B VAL* 1.3 60.7 + - - +
131B PHE* 4.3 6.9 + - - -
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Residues in contact with VAL 130 (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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42B THR* 3.2 3.1 + - - -
43B ASP* 3.0 40.5 + - + +
45B LEU* 6.3 1.6 - - + -
64B ALA* 2.9 36.1 - - + +
65B ILE* 4.3 19.3 - - + -
67B VAL* 5.4 0.4 - - + -
68B ASN* 3.2 27.5 + - + +
82B ALA* 4.4 5.8 - - + -
83B LEU 3.3 11.9 - - - +
84B ILE* 4.6 10.3 - - + -
128B ILE* 5.1 2.7 - - + +
129B SER* 1.3 74.8 - - - +
131B PHE* 1.3 68.3 + - - +
132B LEU* 5.6 0.7 - - + -
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Residues in contact with PHE 131 (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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42A THR* 3.1 29.4 - - - -
83A LEU* 4.4 4.0 - - + -
85A SER* 4.2 8.7 - - - -
129A SER* 3.3 35.9 - - - -
131A PHE* 3.0 61.4 - + + -
41B THR 3.6 2.5 - - - -
42B THR* 3.1 37.7 - - + -
68B ASN* 3.6 0.7 - - - -
82B ALA* 3.1 9.4 - - - +
83B LEU* 2.8 40.9 + - + +
85B SER* 4.0 9.0 - - - -
129B SER* 4.3 6.5 - - - -
130B VAL* 1.3 72.2 - - - +
132B LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 132 (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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131A PHE* 4.7 1.6 - - - -
39B LEU 3.5 1.0 - - - +
40B LEU* 3.5 5.9 - - - +
41B THR* 2.8 41.8 + - + +
65B ILE* 5.9 1.8 - - + -
68B ASN* 3.1 35.0 - - + +
69B VAL* 3.6 22.9 - - + +
72B VAL* 3.3 26.9 - - + -
79B PRO* 4.1 14.4 - - + -
80B LYS 4.6 1.3 - - - +
81B TRP 3.2 18.8 - - - +
82B ALA* 3.7 17.0 - - + -
113B CYS* 4.9 7.2 - - - -
130B VAL* 5.6 0.7 - - + -
131B PHE* 1.3 72.5 - - - +
133B VAL* 1.3 70.5 + - - +
134B GLY 4.1 0.2 - - - -
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Residues in contact with VAL 133 (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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38A LEU* 5.8 0.9 - - + -
40A LEU* 4.0 18.8 - - + -
131A PHE* 3.6 30.3 - - + -
133A VAL* 4.6 1.3 - - + -
38B LEU* 4.3 13.2 - - + -
39B LEU 3.5 2.5 - - - -
40B LEU* 3.6 17.0 - - + -
79B PRO* 3.9 0.5 - - - +
80B LYS* 2.9 28.2 + - - +
81B TRP* 2.9 48.4 + - + +
132B LEU* 1.3 74.8 - - - +
134B GLY* 1.3 67.8 + - - +
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Residues in contact with GLY 134 (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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38B LEU* 3.0 12.7 - - - +
39B LEU* 2.5 50.5 + - - -
72B VAL* 4.2 11.8 - - - +
78B LEU 3.3 11.2 - - - -
80B LYS* 5.0 1.3 - - - -
133B VAL* 1.3 77.6 - - - +
135B GLU* 1.3 59.3 + - - -
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Residues in contact with GLU 135 (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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33A TYR* 2.8 39.3 + - + +
36B LYS* 3.1 34.5 + - + +
37B LYS 4.1 1.6 - - - -
38B LEU* 4.6 3.8 - - + +
77B GLY* 3.6 0.6 - - - -
78B LEU* 3.0 34.6 + - + +
80B LYS* 3.0 38.6 - - + +
134B GLY* 1.3 74.5 - - - -
136B THR* 1.3 61.2 - - - +
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Residues in contact with THR 136 (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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36B LYS* 2.8 28.2 - - - +
37B LYS* 2.9 41.6 + - + +
39B LEU* 3.7 22.9 - - + -
76B GLY 2.8 27.2 + - - -
77B GLY* 3.8 5.2 - - - -
135B GLU* 1.3 77.1 - - - +
137B GLU* 1.3 62.2 + - - +
138B ARG 3.3 12.9 + - - -
139B PHE* 4.2 12.3 - - - +
199B GLN* 4.1 3.2 + - - -
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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