Contacts of the strand formed by residues 134 - 142 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31S ILE* 4.2 1.3 - - - -
78S LEU* 4.1 13.0 - - + -
79S ALA 3.7 24.9 - - - +
80S GLY 3.9 1.1 - - - +
81S LEU 3.4 23.3 - - - +
84S ASP* 3.8 11.2 - - + -
85S ALA* 3.8 23.6 - - + +
88S LEU* 4.0 17.3 - - + -
132S TYR* 4.9 0.2 - - + -
133S GLY* 1.3 79.1 - - - +
135S GLY* 1.3 67.6 + - - +
136S LEU* 4.3 5.6 - - + -
151S PHE* 3.6 9.5 - - - -
153S PRO* 3.0 23.9 - - - +
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Residues in contact with GLY 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ILE* 3.8 17.1 - - - +
78S LEU* 3.5 4.2 - - - -
79S ALA 3.0 34.0 + - - -
134S VAL* 1.3 74.8 - - - +
136S LEU* 1.3 62.0 + - - +
151S PHE 3.4 12.3 - - - -
152S GLN* 4.8 0.9 - - - -
153S PRO* 4.2 0.4 - - - -
165S ILE* 3.6 16.3 - - - +
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Residues in contact with LEU 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S LEU* 4.0 26.9 - - + -
77S SER 3.2 12.3 - - - +
78S LEU* 4.0 15.0 - - + -
85S ALA* 4.1 15.9 - - + -
88S LEU* 3.8 26.9 - - + -
116S LEU* 4.3 10.8 - - + -
134S VAL* 4.3 7.0 - - + -
135S GLY* 1.3 82.1 - - - +
137S LEU* 1.3 65.5 + - - +
138S ILE* 4.1 9.3 + - + +
149S LEU 3.7 0.9 - - - +
150S GLU* 3.6 3.3 - - - +
151S PHE* 2.8 65.1 + - + +
165S ILE* 3.8 1.2 - - - +
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Residues in contact with LEU 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S THR 3.9 13.5 - - - +
38S VAL* 3.5 9.0 - - - +
39S GLY* 3.3 33.2 - - - +
48S LEU* 3.7 10.2 - - + +
76S LEU* 2.9 6.9 - - - -
77S SER* 2.8 53.9 + - - +
136S LEU* 1.3 78.4 - - - +
138S ILE* 1.3 62.4 + - - +
139S ILE 4.1 0.2 - - - -
148S LEU* 4.3 2.9 - - + -
149S LEU 3.3 7.6 - - - +
150S GLU* 4.1 9.0 - - + -
163S THR* 3.6 26.9 - - + +
165S ILE* 3.8 25.4 - - + -
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Residues in contact with ILE 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S MET* 4.5 14.1 - - + -
75S GLY 3.4 8.7 - - - +
76S LEU* 3.8 17.5 - - + -
92S LEU* 5.0 5.2 - - + -
109S VAL* 4.1 21.8 - - + +
112S ALA* 5.2 2.9 - - + -
113S GLY* 5.5 2.2 - - - +
116S LEU* 3.4 32.3 - - + -
136S LEU* 4.5 5.2 - - + +
137S LEU* 1.3 78.5 - - - +
139S ILE* 1.3 66.8 + - - +
147S HIS 3.7 0.9 - - - +
148S LEU* 3.3 3.7 - - - +
149S LEU* 2.7 58.6 + - + +
151S PHE* 4.3 18.4 - - + -
157S VAL* 5.7 1.1 - - + -
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Residues in contact with ILE 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S LEU 5.0 0.2 - - - +
46S ALA* 3.6 43.1 - - + +
47S VAL 4.1 5.6 - - - +
48S LEU* 3.7 34.8 - - + +
74S MET* 3.4 6.4 - - - +
75S GLY 3.0 29.3 + - - +
109S VAL* 4.9 0.2 - - - -
137S LEU 4.1 0.6 + - - -
138S ILE* 1.3 74.6 - - - +
140S GLY* 1.3 58.5 + - - +
147S HIS 3.2 4.3 - - - +
148S LEU* 3.5 28.9 - - + -
213S ALA 4.0 5.8 - - - +
215S VAL* 3.7 11.6 - - + +
221S PHE* 3.7 23.8 - - + -
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Residues in contact with GLY 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S ALA* 4.6 1.0 - - - +
73S HIS 3.0 13.7 - - - -
74S MET* 4.2 0.9 - - - -
109S VAL* 3.8 20.3 - - - +
139S ILE* 1.3 78.3 - - - +
141S TYR* 1.3 60.1 + - - -
145S GLY 3.7 1.2 - - - +
146S ALA* 3.6 3.1 - - - +
147S HIS* 3.0 31.7 + - - +
215S VAL* 3.9 9.9 - - - +
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Residues in contact with TYR 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S ASN 4.2 7.2 + - - -
44S THR* 3.8 21.1 - - - +
73S HIS* 3.0 31.1 + - + +
106S LYS* 5.9 1.2 - - - +
140S GLY* 1.3 72.3 - - - -
142S ASP* 1.3 72.7 + - - +
145S GLY* 3.4 31.6 - - - -
146S ALA* 3.6 10.3 - - + -
215S VAL* 3.9 11.9 - - + +
216S GLY* 3.7 28.9 - - - +
217S LYS* 3.7 43.7 - - + +
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Residues in contact with ASP 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761 GLU* 4.3 8.3 - - - +
73S HIS* 4.4 12.1 - - + +
106S LYS* 5.7 7.2 - - + +
107S LEU 4.5 1.6 - - - +
108S ALA* 3.6 12.6 - - - +
109S VAL* 3.0 33.9 + - + +
110S GLU 4.8 0.5 + - - -
140S GLY 4.1 0.2 - - - -
141S TYR* 1.3 90.0 - - - +
143S LYS* 1.3 60.2 + - - +
144S SER* 2.8 32.8 + - - -
145S GLY 3.1 12.3 + - - -
147S HIS* 3.1 24.7 + - - -
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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