Contacts of the strand formed by residues 127 - 134 (chain A) in PDB entry 1SMB
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TRP* 3.4 8.0 - - - -
70A ALA 2.9 19.9 + - - -
72A TYR 2.7 23.2 + - - -
73A ASP* 4.1 13.2 - - - -
74A GLN* 3.0 39.2 + - - +
119A LYS* 4.3 9.0 - - - -
120A ALA 3.5 8.1 - - - -
121A SER* 4.0 11.2 - - - +
125A GLY 3.6 1.0 + - - -
126A SER* 1.3 72.8 - - - +
128A PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 128 (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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43A SER* 3.5 19.6 - - - +
46A LEU* 3.7 26.5 - - + -
47A ALA* 3.8 14.8 - - - -
50A ARG* 3.6 33.2 - - + -
51A ILE 4.6 0.4 - - - -
52A LEU* 3.6 29.4 - - + -
68A ALA 3.7 2.9 - - - -
69A TRP* 3.5 26.5 - + - -
119A LYS* 3.3 4.0 - - - -
120A ALA 2.8 37.0 + - - +
122A ALA* 3.8 13.5 - - + -
126A SER* 3.4 24.2 - - - -
127A SER* 1.3 76.6 - - - +
129A VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 129 (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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9A PHE* 3.7 31.4 - - + -
13A VAL* 5.6 1.8 - - + -
46A LEU* 5.4 0.7 - - - +
66A ASN 3.8 0.2 - - - +
67A LEU* 3.4 7.3 - - - +
68A ALA* 2.8 42.3 + - + +
74A GLN* 3.5 20.6 - - - +
79A VAL* 4.0 24.5 - - + -
83A TRP* 4.2 9.0 - - + -
117A VAL* 5.0 3.1 - - + -
118A GLY 3.4 8.1 - - - +
119A LYS* 3.8 15.5 - - + -
128A PHE* 1.3 75.1 - - - +
130A VAL* 1.3 70.4 + - - +
131A ALA* 4.3 0.4 - - + -
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Residues in contact with VAL 130 (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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39A ALA* 3.7 22.7 - - + +
42A TYR* 4.0 6.3 - - + -
43A SER* 3.8 28.7 - - - +
46A LEU* 3.8 11.2 - - + -
65A GLU* 4.0 23.8 - - + +
66A ASN 3.6 2.9 - - - -
67A LEU* 3.8 17.7 - - + -
117A VAL* 3.5 4.3 - - - +
118A GLY 2.9 34.1 + - - +
129A VAL* 1.3 82.9 - - - +
131A ALA* 1.3 62.0 + - - +
132A ARG* 4.1 11.9 - - - +
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Residues in contact with ALA 131 (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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13A VAL* 5.5 1.1 - - + -
65A GLU* 3.2 9.0 - - - +
66A ASN 2.9 31.5 + - - +
83A TRP* 3.5 33.1 - - + -
115A MET* 4.1 10.8 - - + -
116A GLY 3.3 7.0 - - - +
117A VAL* 4.6 3.1 - - + +
129A VAL* 5.6 0.4 - - + -
130A VAL* 1.3 73.1 - - - +
132A ARG* 1.3 61.9 + - - +
133A TYR* 3.6 17.7 - - + +
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Residues in contact with ARG 132 (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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35A LEU* 4.7 11.0 - - + +
38A GLU* 3.9 24.6 + - - +
39A ALA* 3.9 17.3 - - + +
42A TYR* 3.4 25.5 - - - +
55A SER* 3.2 30.0 + - - -
57A GLU* 3.7 21.9 + - - +
58A SER 5.9 0.2 - - - +
63A OCS 3.7 31.3 + - - +
64A GLY 3.3 10.1 - - - -
65A GLU* 2.7 24.9 + - - -
115A MET* 3.0 10.6 - - - +
116A GLY* 2.8 37.2 + - - +
130A VAL* 4.1 3.7 - - + +
131A ALA* 1.3 77.2 - - - +
133A TYR* 1.3 60.9 - - - +
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Residues in contact with TYR 133 (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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17A HIS* 2.7 40.5 + + - -
29A LEU* 4.3 5.4 - - + -
35A LEU* 5.2 0.7 - - - -
63A OCS 3.5 8.1 - - - -
64A GLY* 2.8 53.7 + - - -
65A GLU 4.0 0.9 - - - -
66A ASN* 3.0 44.7 + - + -
83A TRP* 3.6 8.3 - - - -
106A ALA* 4.3 21.1 - - + +
107A MET* 3.9 4.3 - - - +
112A THR* 3.8 22.9 - - + +
114A LYS 3.5 2.2 - - - -
115A MET* 3.9 17.3 - - + -
131A ALA* 3.9 12.6 - - + -
132A ARG* 1.3 77.9 - - - +
134A PHE* 1.3 61.8 + - - +
135A PRO 3.8 7.2 - - - +
136A ALA* 5.3 0.4 - - - -
137A GLY 5.4 1.6 - - - +
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Residues in contact with PHE 134 (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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35A LEU* 4.3 15.0 - - + -
62A GLN 3.6 17.7 - - - -
63A OCS 3.3 23.3 - - - +
112A THR* 3.9 0.8 - - - +
113A LYS* 2.9 4.5 + - - +
114A LYS* 2.8 45.7 + - + +
133A TYR* 1.3 75.3 - - - +
135A PRO* 1.3 85.8 - - + +
136A ALA 5.2 0.4 - - - -
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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