Contacts of the strand formed by residues 138 - 143 (chain F) in PDB entry 3IFS
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 PHE 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F SER* 3.8 1.8 - - - -
76F ILE* 3.1 26.9 - - + +
78F LEU* 4.4 9.6 - - + -
133F LEU* 4.3 42.2 - - + -
136F LYS 3.9 12.6 - - - +
137F ASP* 1.3 74.8 - - - +
139F SER* 1.3 74.1 + - - +
140F ILE* 4.2 15.3 - - + -
159F PHE* 4.6 3.6 - - + -
162F LEU* 4.4 7.0 - - + -
163F LEU* 3.6 53.4 - - + +
166F LYS* 3.9 22.9 - - + -
167F TYR* 3.0 5.8 + - - -
175F ARG* 3.0 18.9 + - - -
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Residues in contact with SER 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 4.3 6.5 - - - +
73F ASP* 3.8 4.9 + - - -
74F SER* 2.7 23.3 + - - -
76F ILE 3.1 4.5 + - - +
77F LEU* 3.6 12.7 - - - -
78F LEU* 2.8 34.5 + - - +
138F PHE* 1.3 75.7 + - - +
140F ILE* 1.3 59.8 + - - +
163F LEU* 4.8 0.7 - - - -
175F ARG* 3.3 28.1 + - - +
177F TYR* 4.1 15.8 + - - -
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Residues in contact with ILE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU* 4.2 2.5 - - - -
78F LEU* 3.3 11.0 - - + +
80F VAL* 3.7 26.2 - - + -
138F PHE* 4.2 13.5 - - + -
139F SER* 1.3 77.2 - - - +
141F ASN* 1.3 62.4 + - - +
142F VAL* 3.9 9.4 + - + +
156F PHE* 4.2 19.1 - - + -
159F PHE* 3.7 39.0 - - + +
160F ARG* 4.0 10.3 - - - +
163F LEU* 4.1 15.7 - - + -
175F ARG 2.9 10.1 + - - +
176F ILE* 3.4 7.8 - - + +
177F TYR* 2.9 28.2 + - - +
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Residues in contact with ASN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 6.0 0.2 - - + -
77F LEU* 3.9 20.3 - - + +
78F LEU 2.9 10.5 + - - +
79F VAL* 3.5 5.7 - - + -
80F VAL 2.9 22.7 + - - +
140F ILE* 1.3 72.9 - - - +
142F VAL* 1.3 63.5 + - - +
143F ILE* 3.6 22.2 + - - +
177F TYR* 2.8 29.0 + - + -
179F THR* 3.3 21.6 + - - -
214F PRO 5.1 0.2 - - - +
218F LEU* 3.7 25.9 - - + +
219F PRO* 3.7 15.6 - - - +
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F VAL* 3.7 15.5 - - + +
140F ILE* 3.8 3.9 - - + -
141F ASN* 1.3 72.1 + - - +
143F ILE* 1.3 63.7 + - - +
144F SER* 4.1 3.4 - - - -
152F PRO* 5.3 2.5 - - + +
156F PHE* 3.7 58.1 - - + -
176F ILE* 4.3 6.7 - - + -
177F TYR 3.0 12.6 + - - +
178F ALA* 3.4 11.8 - - + -
179F THR 2.8 26.5 + - - +
187F LEU* 4.0 23.4 - - + +
196F TYR* 5.7 0.2 - - + -
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F VAL* 3.8 18.2 - - + -
80F VAL 2.9 17.0 + - - +
81F GLY* 3.8 4.9 - - - -
82F ILE 4.9 0.2 + - - -
85F SER* 3.3 49.4 - - - +
89F ALA* 6.1 0.4 - - + -
141F ASN* 3.6 31.0 - - - +
142F VAL* 1.3 77.5 - - - +
144F SER* 1.3 64.8 + - - +
152F PRO* 4.9 2.4 - - - +
179F THR* 3.3 13.5 - - + +
201F ILE* 4.2 2.5 - - + -
215F VAL* 3.6 44.4 - - + +
219F PRO* 4.6 1.6 - - + -
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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