Contacts of the strand formed by residues 138 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER* 3.9 1.8 - - - -
76A ILE* 3.2 28.7 - - + +
78A LEU* 4.4 8.7 - - + -
133A LEU* 4.2 40.6 - - + -
136A LYS 3.9 12.3 - - - +
137A ASP* 1.3 73.7 - - - +
139A SER* 1.3 73.7 + - - +
140A ILE* 4.0 18.6 - - + -
159A PHE* 4.6 3.4 - + - -
162A LEU* 4.6 6.3 - - + -
163A LEU* 3.7 42.7 - - + +
166A LYS* 3.6 24.7 - - + -
167A TYR* 3.0 6.1 + - - -
175A ARG* 3.2 24.9 + - - -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS* 5.7 0.2 + - - -
70A ILE* 4.3 7.6 - - - +
73A ASP* 3.9 4.0 + - - -
74A SER* 2.6 23.7 + - - -
76A ILE 3.1 5.1 + - - +
77A LEU* 3.6 13.0 - - - +
78A LEU* 2.9 29.1 + - - +
138A PHE* 1.3 77.5 + - - +
140A ILE* 1.3 65.2 + - - +
163A LEU* 4.9 1.1 - - - -
175A ARG* 3.3 26.0 + - - +
177A TYR* 4.1 15.5 + - - -
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 4.1 2.9 - - - -
78A LEU* 3.3 11.9 - - + +
80A VAL* 3.8 23.6 - - + -
138A PHE* 4.0 15.5 - - + -
139A SER* 1.3 78.1 - - - +
141A ASN* 1.3 62.1 + - - +
142A VAL* 3.9 9.2 - - + +
156A PHE* 4.2 17.7 - - + -
159A PHE* 3.7 37.7 - - + +
160A ARG* 4.1 6.3 - - - +
163A LEU* 4.0 16.8 - - + -
175A ARG 2.8 11.8 + - - +
176A ILE* 3.4 11.4 - - + -
177A TYR* 2.8 28.5 + - - +
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 6.0 0.2 - - + -
77A LEU* 3.9 20.7 - - + +
78A LEU 2.9 8.2 + - - +
79A VAL* 3.5 5.8 - - + -
80A VAL 2.9 23.0 + - - +
140A ILE* 1.3 72.8 - - - +
142A VAL* 1.3 62.7 + - - +
143A ILE* 3.5 22.8 + - - +
177A TYR* 2.8 28.3 + - + -
179A THR* 3.4 21.6 + - - -
214A PRO 5.1 0.3 - - - +
218A LEU* 3.7 21.3 - - + +
219A PRO* 3.6 21.1 - - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.6 18.8 - - + +
140A ILE* 3.8 3.0 - - + -
141A ASN* 1.3 72.3 + - - +
143A ILE* 1.3 64.4 + - - +
144A SER* 4.2 3.8 - - - -
152A PRO* 5.1 3.1 - - + +
156A PHE* 3.9 48.9 - - + -
176A ILE* 4.3 6.1 - - + -
177A TYR 2.8 15.2 + - - +
178A ALA* 3.4 7.6 - - + -
179A THR 2.9 26.2 + - - +
187A LEU* 3.7 35.1 - - + +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.9 16.2 - - + -
80A VAL 2.9 18.1 + - - +
81A GLY* 3.8 5.0 - - - -
82A ILE 4.9 0.2 + - - -
85A SER* 3.4 47.8 - - - +
89A ALA* 6.0 0.9 - - + -
141A ASN* 3.5 29.2 - - - +
142A VAL* 1.3 79.5 - - - +
144A SER* 1.3 66.5 + - - +
152A PRO* 4.8 1.9 - - - +
179A THR* 3.4 15.0 - - + +
201A ILE* 4.2 2.0 - - + -
215A VAL* 3.5 46.7 - - + +
219A PRO* 4.5 2.2 - - + -
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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