Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 3SDI
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 VAL 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.6 6.7 - - - +
78A TYR* 3.9 14.4 - - + -
79A SER 3.6 5.6 - - - +
81A MET 3.1 34.5 - - - +
84A ASP* 4.0 2.9 - - + -
85A TYR* 4.0 10.1 - - + +
88A LEU* 3.6 31.6 - - + -
120A MET* 3.5 12.6 - - + +
132A PHE* 3.2 6.8 + - + -
133A GLY* 1.3 83.1 - - - +
135A SER* 1.3 60.4 + - - +
136A LEU* 3.7 17.9 - - + -
153A PRO* 3.3 20.8 - - - +
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Residues in contact with SER 135 (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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28A LEU* 4.8 2.1 - - - +
31A VAL* 3.7 23.0 - - - +
78A TYR* 3.2 4.5 - - - +
79A SER 3.1 31.1 + - - -
134A VAL* 1.3 72.1 - - - +
136A LEU* 1.3 63.7 + - - +
150A GLN* 4.1 1.4 + - - -
151A VAL 3.2 7.7 + - - -
152A ASP* 2.5 29.1 + - - -
153A PRO* 3.7 8.3 - - - +
165A ILE* 3.4 19.9 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 6.3 0.7 - - + -
76A ALA* 5.2 5.6 - - + -
77A VAL 3.3 7.0 - - - +
78A TYR* 3.9 2.9 - - + -
85A TYR* 3.7 28.7 - - + -
88A LEU* 4.3 14.4 - - + -
89A VAL* 6.5 0.9 - - + -
92A SER* 5.5 0.9 - - - +
116A VAL* 3.8 28.9 - - + -
120A MET* 4.5 6.1 - - - -
134A VAL* 3.7 27.4 - - + -
135A SER* 1.3 75.1 - - - +
137A LEU* 1.3 65.8 + - - +
138A ILE* 4.1 21.8 - - + -
149A TYR 3.7 0.2 - - - +
150A GLN* 3.3 5.7 - - - +
151A VAL* 2.8 41.9 + - + +
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Residues in contact with LEU 137 (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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37A SER 4.1 0.7 - - - +
38A LEU* 3.4 43.5 - - - +
39A GLY* 3.5 6.5 - - - +
48A ILE* 4.7 4.6 - - + +
76A ALA* 3.3 3.5 - - - -
77A VAL* 2.9 44.7 + - + +
136A LEU* 1.3 79.5 - - - +
138A ILE* 1.3 62.5 + - - +
139A ALA 4.2 0.4 + - - -
148A LEU* 4.3 10.5 - - + -
149A TYR 3.2 4.5 - - - +
150A GLN* 3.7 28.0 - - + +
163A THR* 3.7 22.4 - - + +
165A ILE* 3.7 24.8 - - + +
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Residues in contact with ILE 138 (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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70A LEU* 4.5 8.1 - - + -
74A ILE* 3.6 27.1 - - + -
75A GLY 3.4 3.8 - - - +
76A ALA* 3.8 13.9 - - + -
109A THR* 4.3 6.4 - - + +
112A LEU* 5.8 2.2 - - + -
113A VAL* 3.8 34.3 - - + +
116A VAL* 4.3 17.7 - - + -
136A LEU* 4.1 19.1 - - + -
137A LEU* 1.3 78.7 - - - +
139A ALA* 1.3 62.1 + - - +
147A SER 4.1 0.3 - - - +
148A LEU* 3.4 2.6 - - - -
149A TYR* 2.8 42.4 + - - +
151A VAL* 4.0 18.6 - - + -
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Residues in contact with ALA 139 (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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46A VAL* 3.4 31.6 - - + -
48A ILE* 3.8 22.2 - - + +
74A ILE* 3.4 4.5 - - - +
75A GLY 2.8 33.4 + - - +
137A LEU 4.2 0.8 + - - -
138A ILE* 1.3 75.5 - - - +
140A GLY* 1.3 59.1 + - - +
147A SER 3.3 4.9 - - - +
148A LEU* 4.2 2.2 - - + +
215A ILE* 3.5 15.7 - - + +
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Residues in contact with GLY 140 (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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46A VAL* 4.5 0.7 - - - +
73A ASP 3.0 12.8 - - - -
74A ILE* 4.1 2.5 - - - -
109A THR* 3.3 21.3 + - - +
139A ALA* 1.3 74.6 - - - +
141A HIS* 1.3 59.0 + - - -
147A SER* 3.0 36.9 + - - +
215A ILE* 3.6 11.1 - - - +
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Residues in contact with HIS 141 (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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73A ASP* 2.9 29.4 + - - +
74A ILE* 4.8 2.6 - - - +
107A PRO 5.4 0.9 - - - +
109A THR* 4.1 3.4 + - - -
140A GLY* 1.3 74.9 - - - +
142A ASP* 1.3 94.1 + - - +
143A GLU* 4.1 8.4 + - - -
146A GLY* 3.5 26.2 - - - -
147A PHE* 3.7 28.8 - + + -
215A ILE* 3.5 10.5 - - + +
220A ARG* 3.0 53.2 + - - -
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Residues in contact with ASP 142 (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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73A ASP* 5.3 2.5 - - - -
106A TYR 6.1 0.2 - - - +
107A PRO 5.0 1.6 - - - +
108A PRO* 3.3 22.5 - - + +
109A THR* 3.2 26.2 + - - -
110A LYS 4.9 0.7 + - - -
141A HIS* 1.3 88.0 - - - +
143A GLU* 1.3 67.5 + - - +
144A PHE* 3.4 4.2 + - - +
145A ASN* 2.7 51.6 + - - +
146A GLY* 2.9 28.5 + - - +
147A SER* 4.8 0.7 - - - +
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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