Contacts of the strand formed by residues 3201 - 3206 (chain C) in PDB entry 1F38
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 ILE3201 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3136C VAL* 3.2 21.8 - - + +
3137C ALA 4.3 0.2 - - - -
3138C VAL* 3.5 41.3 - - + +
3195C LEU* 5.7 2.5 - - + -
3198C ILE* 4.4 14.1 - - + -
3199C PRO 4.4 0.7 - - - +
3200C ASP* 1.3 79.5 - - - +
3202C ASP* 1.3 62.9 + - - +
3203C ILE 3.9 5.4 - - - +
3204C ALA* 3.9 13.2 - - + -
3220C ILE* 4.0 17.5 - - + +
3223C LYS* 2.8 31.1 + - + +
3224C LEU* 3.5 14.6 - - + +
3225C LYS* 2.9 26.4 + - - -
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Residues in contact with ASP3202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3134C ASN 4.2 1.7 - - - +
3135C ASP* 3.2 37.8 - - + +
3136C VAL* 2.7 29.3 + - - +
3201C ILE* 1.3 74.9 - - - +
3203C ILE* 1.3 63.3 + - - +
3224C LEU* 4.4 1.1 - - - -
3225C LYS* 3.2 38.0 + - - +
3226C PRO 5.2 2.8 - - - +
3228C GLY* 3.0 11.3 - - - -
3229C ARG* 2.9 34.8 + - - +
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Residues in contact with ILE3203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3129C ALA* 3.8 37.5 - - + +
3131C PRO* 3.9 20.6 - - + -
3135C ASP* 4.0 15.3 - - + +
3136C VAL 3.4 2.1 + - - +
3137C ALA* 3.1 17.1 - - + -
3138C VAL* 3.1 25.6 + - - +
3151C LEU* 4.5 8.1 - - + -
3155C VAL* 4.2 9.2 - - + -
3201C ILE* 3.9 3.5 - - - +
3202C ASP* 1.3 88.9 - - + +
3204C ALA* 1.3 64.2 + - - +
3205C VAL* 4.2 17.5 - - + -
3229C ARG* 3.5 23.8 - - + +
3231C ILE* 5.3 1.8 - - + -
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Residues in contact with ALA3204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3138C VAL* 3.7 17.5 - - + -
3201C ILE* 3.9 4.0 - - + -
3203C ILE* 1.3 74.6 - - - +
3205C VAL* 1.3 63.5 + - - +
3206C VAL 4.1 0.2 - - - -
3220C ILE* 3.4 39.0 - - + -
3224C LEU* 4.8 0.7 - - + -
3229C ARG 2.8 14.7 + - - +
3230C ILE* 3.3 7.2 - - + +
3231C ILE* 2.8 27.0 + - - +
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Residues in contact with VAL3205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3125C ILE* 4.0 32.5 - - + -
3129C ALA* 5.4 0.7 - - + -
3138C VAL 3.0 9.6 + - - +
3139C ASP* 3.5 18.3 - - - +
3140C VAL* 2.9 27.0 + - - +
3147C VAL* 4.2 23.6 - - + -
3151C LEU* 4.6 6.7 - - + -
3203C ILE* 4.2 17.0 - - + -
3204C ALA* 1.3 78.2 - - - +
3206C VAL* 1.3 69.6 + - - +
3207C GLY* 4.1 1.3 - - - +
3231C ILE* 3.2 16.8 - - + +
3233C THR* 4.7 5.6 - - - +
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Residues in contact with VAL3206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3140C VAL* 3.7 16.2 - - + -
3205C VAL* 1.3 80.9 - - - +
3207C GLY* 1.3 69.1 + - - +
3209C SER* 4.3 10.5 - - - -
3213C LEU* 4.0 23.3 - - + -
3216C ILE* 4.3 7.6 - - + -
3217C LEU* 4.2 14.6 - - + -
3220C ILE* 3.7 30.5 - - + -
3230C ILE* 4.8 3.8 - - + -
3231C ILE 2.8 13.4 + - - +
3232C VAL* 3.4 10.6 - - + +
3233C THR* 2.8 27.0 + - - -
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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