Contacts of the strand formed by residues 76 - 80 (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 ILE 76 (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* 3.3 7.8 - - - -
75A ASP* 1.3 88.0 - - + +
77A LEU* 1.3 75.2 + - - +
78A LEU* 4.2 1.8 - - - +
112A PRO* 4.2 1.8 - - - -
113A GLN* 3.2 36.8 - - + +
115A LEU* 3.7 26.5 - - + -
132A VAL 3.8 21.8 - - - +
133A LEU* 3.9 23.8 - - + -
136A LYS* 4.0 17.3 - - + -
137A ASP 3.2 1.6 + - - -
138A PHE* 3.2 12.7 - - + +
139A SER 3.1 23.6 + - - -
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Residues in contact with LEU 77 (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* 4.3 15.9 - - + -
76A ILE* 1.3 75.2 - - - +
78A LEU* 1.3 60.4 + - - +
79A VAL* 3.8 17.4 + - + -
112A PRO* 4.3 0.6 - - + +
113A GLN 2.8 11.6 + - - +
114A VAL* 3.4 9.3 - - + +
115A LEU 2.9 26.9 + - - +
139A SER* 3.6 27.4 - - - +
140A ILE 4.1 0.7 - - - -
141A ASN* 3.9 27.4 - - + +
218A LEU* 5.3 1.1 - - + -
219A PRO* 4.0 18.6 - - + -
222A VAL* 4.0 40.2 - - + -
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Residues in contact with LEU 78 (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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76A ILE* 4.0 4.9 - - + -
77A LEU* 1.3 71.3 - - - +
79A VAL* 1.3 61.9 + - - +
80A VAL* 3.8 4.6 + - + -
115A LEU* 3.5 21.1 - - + +
117A VAL* 3.7 19.7 - - + -
129A LEU* 3.7 25.4 - - + -
133A LEU* 4.5 7.4 - - + -
138A PHE* 4.4 13.9 - - + -
139A SER 2.9 15.1 + - - +
140A ILE* 3.3 15.6 - - + +
141A ASN 2.9 25.2 + - - +
159A PHE* 3.7 43.1 - - + -
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Residues in contact with VAL 79 (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* 4.0 16.8 - - + -
78A LEU* 1.3 74.5 - - - +
80A VAL* 1.3 65.5 + - - +
81A GLY 3.9 0.8 + - - +
85A SER 4.4 7.6 - - - +
86A TYR* 5.6 0.9 - - + -
89A ALA* 5.7 1.3 - - + -
114A VAL* 3.8 26.9 - - + -
115A LEU 2.8 8.7 + - - -
116A PHE* 3.4 30.7 - - + +
117A VAL 2.9 26.5 + - - +
141A ASN* 3.5 6.1 - - + +
143A ILE* 3.9 26.5 - - + -
219A PRO* 4.1 14.1 - - + -
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Residues in contact with VAL 80 (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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78A LEU* 4.3 7.6 - - + +
79A VAL* 1.3 76.1 - - - +
81A GLY* 1.3 61.1 + - - +
117A VAL* 3.2 24.9 - - + +
140A ILE* 3.8 24.9 - - + -
141A ASN 2.9 7.7 + - - -
142A VAL* 4.1 13.7 - - + +
143A ILE* 2.9 32.2 + - - +
152A PRO* 3.5 32.7 - - + +
155A ALA* 4.1 4.9 - - + +
156A PHE* 4.0 21.8 - - + +
159A PHE* 5.5 1.3 - - + -
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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