Contacts of the strand formed by residues 119 - 122 (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 GLY 119 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I THR 4.0 2.0 + - - -
63I VAL* 3.4 2.7 - - - +
64I GLY 3.0 24.9 + - - -
117I VAL* 3.4 3.1 - - - +
118I ASP* 1.3 82.1 - - - +
120I ILE* 1.3 68.5 + - - +
140I VAL* 4.2 2.9 - - - -
141I PRO 3.4 11.0 - - - -
305I LEU* 3.9 21.8 - - - -
309I MET* 4.0 3.2 - - - -
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Residues in contact with ILE 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLY* 3.2 15.3 - - - +
66I ILE* 4.1 19.5 - - + -
109I LEU* 4.4 13.9 - - + -
112I MET* 3.6 32.5 - - + -
113I LEU* 3.8 19.3 - - + -
117I VAL* 4.2 7.2 - - + -
119I GLY* 1.3 81.7 - - - +
121I ILE* 1.3 77.3 + - - +
122I PHE* 4.0 3.8 - - + +
140I VAL* 4.1 6.3 - - + -
141I PRO 2.9 8.9 + - - +
142I VAL* 3.2 19.7 - - + +
143I VAL* 2.9 28.4 + - - +
305I LEU* 3.8 3.4 - - - +
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Residues in contact with ILE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 3.6 8.7 - - + -
64I GLY 3.3 4.2 + - - -
65I VAL* 3.3 19.1 - - + +
66I ILE 3.0 24.1 + - - -
82I ILE* 4.2 23.3 - - + -
120I ILE* 1.3 74.9 - - - +
122I PHE* 1.3 59.9 + - - +
123I MET* 4.5 4.0 - - + -
143I VAL* 3.2 8.7 - - + +
145I ALA* 3.6 29.6 - - + -
301I ALA* 4.2 18.6 - - + +
302I MET* 3.3 19.3 - - + -
305I LEU* 3.2 35.0 - - + -
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Residues in contact with PHE 122 (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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66I ILE* 3.6 37.7 - - + -
105I GLU* 3.4 44.9 - - + -
109I LEU* 5.5 2.7 - - + -
120I ILE* 3.7 4.9 + - + -
121I ILE* 1.3 71.2 - - - +
123I MET* 1.3 77.1 + - - +
124I SER* 3.6 14.4 - - - -
127I VAL* 4.0 10.8 - - + -
131I HIS* 4.7 9.6 - - - -
135I LEU* 4.4 20.6 - - + -
142I VAL* 4.0 15.3 - - + -
143I VAL 3.0 6.7 + - - -
144I LEU* 3.1 35.6 - - + +
145I ALA 3.0 23.2 + - - -
147I SER* 3.5 2.4 + - - -
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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