Contacts of the strand formed by residues 142 - 145 (chain I) in PDB entry 1SXG
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 142 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I LEU* 3.7 33.4 - - + -
120I ILE* 3.2 19.7 - - + +
122I PHE* 4.0 20.6 - - + -
135I LEU* 4.2 20.0 - - + +
138I SER* 4.0 11.9 - - - +
140I VAL* 3.3 14.6 - - + +
141I PRO* 1.3 79.9 - - - +
143I VAL* 1.3 66.0 + - - +
144I LEU* 4.9 2.4 - - + +
154I ILE* 5.1 3.8 - - - +
155I PRO* 3.6 20.4 - - - +
308I TYR* 6.0 1.0 - - - -
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Residues in contact with VAL 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I ILE 2.9 4.4 + - - +
121I ILE* 3.2 12.7 - - + +
122I PHE 3.0 20.5 + - - -
142I VAL* 1.3 77.4 - - - +
144I LEU* 1.3 74.2 + - - +
155I PRO* 3.2 27.6 - - + +
157I VAL* 4.4 1.6 - - + -
301I ALA* 3.9 21.5 - - + +
304I LEU* 4.1 15.9 - - + -
305I LEU* 3.6 42.2 - - + +
308I TYR* 5.1 3.1 - - + -
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Residues in contact with LEU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I PHE* 3.1 46.7 - - + +
127I VAL* 4.1 16.4 - - + -
135I LEU* 4.1 14.6 - - + -
142I VAL* 4.9 2.9 - - + +
143I VAL* 1.3 82.1 - - - +
145I ALA* 1.3 62.6 + - - +
146I ALA 4.3 0.2 - - - -
147I SER* 3.8 21.5 - - - +
148I ILE 4.7 0.2 - - - -
149I GLU* 4.2 9.6 - - + -
154I ILE* 3.6 28.9 - - + -
155I PRO 2.7 15.1 + - - +
156I SER* 3.8 16.2 - - - -
157I VAL* 3.2 22.1 + - - +
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Residues in contact with ALA 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I TYR* 5.7 0.3 - - - -
78I LEU* 4.6 4.5 - - + -
82I ILE* 5.2 1.3 - - + -
121I ILE* 3.6 25.1 - - + -
122I PHE 3.0 7.3 + - - -
123I MET* 3.8 24.1 - - - +
144I LEU* 1.3 77.5 - - - +
146I ALA* 1.3 73.1 + - - +
147I SER* 3.1 6.7 + - - -
157I VAL 3.6 4.7 - - - -
297I ILE* 4.0 16.8 - - + -
301I ALA* 4.6 6.5 - - + -
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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