Contacts of the strand formed by residues 107 - 116 (chain B) in PDB entry 3SKU
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 ALA 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B PRO* 4.2 4.3 - - + -
48B PHE* 3.8 18.3 - - + -
100B PHE* 4.0 15.0 - - + -
101B ARG 3.8 5.8 - - - -
102B MET* 4.3 14.4 - - - +
106B CYS* 1.3 75.6 - - - +
108B ILE* 1.3 64.5 + - - +
202B CYS* 3.2 5.2 - - - -
203B LEU* 2.7 32.5 + - - +
208B TYR* 3.8 15.7 - - + +
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Residues in contact with ILE 108 (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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100B PHE* 2.9 28.1 - - - -
101B ARG* 3.0 39.2 + - + +
102B MET 4.8 1.6 - - - +
107B ALA* 1.3 80.8 - - - +
109B PRO* 1.3 81.3 - - + +
110B ILE* 3.5 3.3 + - + +
137B TYR* 4.0 12.3 - - + -
197B ILE* 3.6 45.3 - - + -
201B ALA 4.1 6.5 - - - +
202B CYS* 3.8 23.1 - - + +
217B ILE* 5.8 0.2 - - + -
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.3 29.8 - - + -
99B TRP 3.6 6.3 - - - +
100B PHE* 4.0 5.6 - - + -
108B ILE* 1.3 92.7 - - + +
110B ILE* 1.3 62.7 + - - +
112B VAL* 4.8 2.9 - - + -
136B ASN* 3.8 10.6 + - - +
201B ALA 4.7 0.7 - - - +
203B LEU* 3.3 15.5 - - + -
208B TYR* 3.2 22.2 - - - +
217B ILE* 3.3 30.1 - - + +
219B MET* 3.7 16.1 - - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 2.7 19.9 + - + +
100B PHE 4.1 4.5 - - - +
101B ARG* 3.5 31.2 - - + +
108B ILE* 4.0 3.1 - - + +
109B PRO* 1.3 73.2 - - - +
111B THR* 1.3 59.5 + - - +
135B TRP* 3.2 12.3 - - + -
136B ASN 2.9 32.2 + - - +
137B TYR* 6.5 0.2 - - + -
138B TYR* 3.3 68.6 - - + -
151B PHE* 4.1 9.9 - - + -
164B TYR* 4.0 13.5 - - + -
219B MET* 3.1 7.7 - - - +
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Residues in contact with THR 111 (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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97B ILE 5.1 1.8 - - - +
98B ALA* 3.5 4.0 - - - -
99B TRP* 2.8 60.4 + - + +
110B ILE* 1.3 79.9 - - - +
112B VAL* 1.3 66.9 + - - +
113B MET* 4.8 18.0 - - + +
134B ARG 2.9 7.1 + - - -
135B TRP* 2.9 49.8 + - + -
144B VAL* 5.0 1.8 - - + -
151B PHE* 4.5 1.6 - - + -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.6 32.8 - - + -
45B PRO* 5.1 2.7 - - + -
96B THR* 4.6 7.9 - - + -
97B ILE 3.7 5.8 - - - +
98B ALA* 4.8 4.0 - - + +
99B TRP 5.9 0.2 - - - +
100B PHE* 6.4 0.2 - - + -
109B PRO* 4.8 2.7 - - + -
111B THR* 1.3 79.1 + - - +
113B MET* 1.3 68.6 + - - +
114B GLU* 4.1 24.5 - - + +
131B THR* 4.0 1.6 + - - -
133B PRO* 3.6 1.6 - - - +
134B ARG* 2.7 49.6 + - + +
214B VAL* 4.1 3.4 - - + -
219B MET* 3.5 31.0 - - + -
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Residues in contact with MET 113 (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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96B THR* 3.3 3.5 - - - +
97B ILE* 2.8 50.9 + - + +
111B THR* 4.8 11.0 - - + +
112B VAL* 1.3 84.4 - - - +
114B GLU* 1.3 62.1 + - - +
115B TYR* 4.0 29.8 - - + +
131B THR* 3.3 6.1 - - - +
133B PRO* 3.7 33.0 - - + -
135B TRP* 5.7 1.6 - - - -
144B VAL* 3.5 34.8 - - + -
148B ASN* 4.0 15.3 - - - +
225B PRO* 4.5 13.9 - - - -
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Residues in contact with GLU 114 (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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40B ILE* 3.2 14.6 + - + +
41B GLN* 2.7 51.5 + - + +
43B GLY 4.1 12.1 - - - +
44B LEU* 5.1 1.2 - - - +
45B PRO* 4.9 2.8 - - - +
95B LEU 3.6 7.2 - - - +
96B THR* 4.0 16.5 - - + +
112B VAL* 4.1 18.3 - - + +
113B MET* 1.3 78.1 - - - +
115B TYR* 1.3 64.5 + - - +
130B ARG* 3.7 1.9 - - - -
131B THR* 2.5 55.6 + - + +
134B ARG* 6.4 0.2 - - + -
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Residues in contact with TYR 115 (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 ARG* 5.3 3.4 - - - -
40B ILE* 4.3 4.7 - - - +
41B GLN* 5.3 1.0 + - - +
94B ASN* 3.6 5.7 - - - +
95B LEU* 2.9 72.7 + - + +
97B ILE* 3.9 17.4 - - + +
113B MET* 4.0 36.7 - - + +
114B GLU* 1.3 79.2 - - - +
116B THR* 1.3 64.3 + - - +
118B CYS* 3.7 19.1 - - - -
125B GLY* 4.0 27.1 - - - -
127B CYS* 4.4 1.6 - - + -
129B ILE 3.8 3.8 - - - -
130B ARG* 4.4 24.9 - - + -
148B ASN* 4.3 14.2 + - - +
225B PRO* 5.6 1.7 - - - +
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Residues in contact with THR 116 (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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40B ILE* 4.1 21.8 - - + +
93B TYR 4.0 3.1 - - - -
94B ASN* 2.7 22.3 + - - -
115B TYR* 1.3 76.6 - - - +
117B GLU* 1.3 78.3 + - + +
118B CYS* 3.2 2.9 + - - -
127B CYS* 3.7 2.4 - - - +
128B PRO* 3.7 9.2 - - - +
129B ILE* 3.2 49.5 + - + +
1307B NAG 4.2 9.4 + - - +
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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