Contacts of the strand formed by residues 134 - 142 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ILE* 3.7 6.5 - - - +
78P VAL* 4.6 2.0 - - + -
79P ALA 3.5 4.9 - - - +
80P GLY* 4.4 2.5 - - - -
81P LEU 3.3 26.0 - - - +
84P ASP* 3.9 6.7 - - + -
85P ALA* 3.7 19.5 - - + +
88P LEU* 4.6 2.9 - - + -
120P LYS* 3.7 10.2 + - - +
132P PHE* 3.0 12.7 + - + +
133P GLY* 1.3 81.8 - - - +
135P SER* 1.3 67.6 + - - +
136P PHE* 3.5 43.3 - - + -
153P PRO* 3.3 21.1 - - - +
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Residues in contact with SER 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P LEU* 4.7 2.8 - - - +
31P ILE* 3.6 25.3 - - - +
77P ALA 3.7 0.3 - - - +
78P VAL* 3.7 3.3 - - - -
79P ALA* 2.7 39.5 + - - +
134P VAL* 1.3 73.3 - - - +
136P PHE* 1.3 62.5 + - - +
151P SER 3.1 8.3 - - - -
152P ASN* 3.4 24.3 - - - +
165P VAL* 4.4 21.8 - - - +
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Residues in contact with PHE 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P VAL* 4.0 17.5 - - + -
77P ALA 3.3 4.3 - - - -
78P VAL* 3.4 33.4 - - + -
85P ALA* 4.2 10.3 - - + -
88P LEU* 4.0 30.1 - - + -
89P ILE* 4.4 7.9 - - + -
116P LEU* 4.2 8.5 - - + -
120P LYS* 3.4 20.0 - - - -
134P VAL* 3.5 22.7 - - + -
135P SER* 1.3 75.5 - - - +
137P ILE* 1.3 63.1 + - - +
138P TYR* 3.3 39.9 - + + -
150P THR* 3.2 10.1 + - - -
151P SER* 2.8 31.1 + - - +
165P VAL* 4.8 1.1 - - - +
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Residues in contact with ILE 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P ALA* 3.4 38.6 - - + +
38P ILE 3.9 1.3 - - - +
39P GLY* 3.8 16.2 - - - +
48P LEU* 4.0 11.9 - - + +
76P VAL* 3.0 6.6 - - - +
77P ALA* 2.8 43.0 + - + +
136P PHE* 1.3 76.5 - - - +
138P TYR* 1.3 62.4 + - - +
139P ALA 4.0 0.5 + - - -
148P LEU* 3.8 25.4 - - + -
149P TYR 3.2 9.6 - - - +
150P THR* 4.2 4.0 - - - +
163P ILE* 4.2 13.5 - - + +
164P SER* 4.4 0.4 - - - -
165P VAL* 3.6 28.9 - - + +
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Residues in contact with TYR 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P LEU* 4.5 2.2 - - + -
74P ILE* 5.0 4.0 - - + -
75P ALA 3.6 3.8 - - - +
76P VAL* 3.1 29.4 - - + -
109P VAL* 5.0 4.0 - - + -
112P LEU* 4.3 11.2 - - + -
113P VAL* 3.5 36.7 + - + -
116P LEU* 3.3 40.3 - - + +
120P LYS* 4.4 0.2 + - - -
136P PHE* 3.3 17.8 - + + -
137P ILE* 1.3 72.6 - - - +
139P ALA* 1.3 60.8 + - - +
140P GLY 4.1 0.2 - - - -
147P GLN 3.5 1.4 - - - +
148P LEU* 3.2 11.4 - - - +
149P TYR* 2.6 60.8 + - + -
150P THR 4.2 0.2 - - - -
151P SER* 3.0 37.3 + - - -
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Residues in contact with ALA 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ILE* 3.7 26.7 - - + -
48P LEU* 3.9 27.8 - - + +
74P ILE* 3.3 3.8 - - - +
75P ALA 2.8 38.0 + - - +
137P ILE 4.0 1.2 + - - -
138P TYR* 1.3 72.8 - - - +
140P GLY* 1.3 58.6 + - - +
147P GLN 3.7 4.5 - - - -
148P LEU* 4.3 0.9 - - + -
215P ILE* 3.2 19.0 - - + +
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Residues in contact with GLY 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ILE* 3.5 6.7 - - - +
73P LYS 3.1 12.1 - - - -
74P ILE* 4.2 3.4 - - - -
109P VAL* 3.8 20.9 - - - +
138P TYR 4.1 0.4 - - - -
139P ALA* 1.3 75.6 - - - +
141P TYR* 1.3 60.8 + - - -
145P GLY 3.7 0.2 - - - +
146P TYR* 3.5 3.8 - - - -
147P GLN* 2.9 34.7 + - - -
215P ILE* 4.2 3.6 - - - -
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Residues in contact with TYR 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P LYS* 3.0 39.8 + - + +
74P ILE* 5.1 0.5 - - - +
107P ILE 5.5 1.0 - - - +
109P VAL* 3.8 6.4 - - - +
140P GLY* 1.3 75.4 - - - -
142P ASP* 1.3 80.6 + - - +
143P ASP* 4.3 7.4 - - + -
145P GLY* 3.5 28.6 - - - -
146P TYR* 3.8 33.2 - + + -
215P ILE* 4.6 1.6 - - + -
216P LYS* 3.4 36.3 + - - -
219P VAL* 3.5 38.1 - - - -
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Residues in contact with ASP 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P LYS* 5.3 3.6 - - + -
106P ASP 6.0 0.4 - - - +
107P ILE 4.9 2.5 - - - +
108P PRO* 3.6 20.1 - - + +
109P VAL* 3.2 23.4 + - + +
110P GLU 4.7 0.3 + - - -
141P TYR* 1.3 89.3 - - - +
143P ASP* 1.3 61.7 + - - +
144P ARG* 2.7 37.2 + - - +
145P GLY* 2.9 32.0 + - - -
147P GLN* 3.1 19.9 + - - +
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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