Contacts of the helix formed by residues 3096 - 3105 (chain C) in PDB entry 1F5T
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 LYS3096 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3092C LEU* 3.7 10.8 - - + +
3093C ASP* 2.9 41.5 + - + +
3095C ASN* 1.3 80.9 - - + +
3097C VAL* 1.3 60.6 + - - +
3098C HIS 3.8 0.7 - - - -
3099C ASP* 4.6 10.5 - - - +
3100C GLU* 3.6 20.4 + - - +
4111D GLU* 3.5 34.8 - - + +
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Residues in contact with VAL3097 (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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3083C GLU* 3.4 39.7 - - + +
3086C LEU* 3.7 11.2 - - + +
3087C THR* 4.4 8.1 - - - -
3092C LEU* 3.7 21.1 - - + +
3093C ASP 2.9 19.7 - - - +
3094C ILE* 3.5 27.6 - - + +
3095C ASN 3.2 3.2 - - - -
3096C LYS* 1.3 78.8 - - - +
3098C HIS* 1.3 68.6 + - - +
3099C ASP 3.4 0.4 - - - -
3100C GLU 3.5 0.7 + - - -
3101C ALA* 3.0 19.9 + - - +
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Residues in contact with HIS3098 (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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256C NI 1.9 38.7 - - + +
3013C ARG* 3.8 19.0 + - - -
3017C GLU* 4.7 3.5 + - - -
3079C HIS* 2.6 17.4 + + - -
3083C GLU* 2.0 22.5 + - - +
3094C ILE 4.8 1.0 + - - -
3095C ASN 4.6 4.0 + - - +
3097C VAL* 1.3 76.7 - - - +
3099C ASP* 1.3 57.8 + - - +
3101C ALA* 2.9 5.9 + - - +
3102C ASP* 2.7 38.8 + - + +
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Residues in contact with ASP3099 (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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3095C ASN 4.2 14.2 - - - +
3096C LYS* 4.6 8.4 - - + +
3097C VAL 3.4 0.4 - - - -
3098C HIS* 1.3 79.8 - - - +
3100C GLU* 1.3 65.0 + - - +
3102C ASP* 2.7 25.6 + - - +
3103C ARG* 3.4 16.6 + - - +
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Residues in contact with GLU3100 (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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3086C LEU* 3.8 16.6 - - + -
3092C LEU* 4.4 2.0 - - + +
3096C LYS 3.6 17.4 + - - +
3097C VAL 3.5 4.4 + - - +
3098C HIS 3.3 0.4 - - - -
3099C ASP* 1.3 79.0 - - - +
3101C ALA* 1.3 62.6 + - - +
3103C ARG* 2.9 33.9 + - - +
3104C TRP* 2.9 47.7 + - - +
4108D MET* 3.6 1.4 - - - -
4109D SER* 2.9 33.9 + - - -
4112D VAL* 3.2 27.6 - - + +
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Residues in contact with ALA3101 (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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3079C HIS* 3.7 19.1 + - + +
3082C ALA* 4.1 7.1 - - + +
3083C GLU* 3.5 33.0 - - + +
3086C LEU* 3.8 5.8 - - + +
3097C VAL 3.0 13.8 + - - +
3098C HIS 2.9 10.9 + - - +
3100C GLU* 1.3 72.9 - - - +
3102C ASP* 1.3 54.0 + - - +
3103C ARG 3.0 10.4 + - - -
3104C TRP* 4.0 1.3 - - - +
3105C GLU* 3.0 28.8 + - - +
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Residues in contact with ASP3102 (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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255C NI 1.7 87.0 - - - +
3004C LEU* 6.1 0.2 - - - +
3010C MET* 2.7 14.6 - - - +
3013C ARG* 4.2 8.5 + - - +
3079C HIS* 4.4 3.6 - - + -
3098C HIS* 2.7 19.3 + - + +
3099C ASP* 2.7 18.8 + - - +
3101C ALA* 1.3 69.9 - - - +
3103C ARG* 1.3 55.7 + - + +
3105C GLU* 3.0 9.6 - - - -
3106C HIS* 2.8 1.7 + - - -
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Residues in contact with ARG3103 (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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3002C LYS 5.8 0.7 - - - -
3003C ASP 5.7 4.0 - - - +
3005C VAL* 4.1 16.2 - - + +
3099C ASP* 3.8 19.5 + - - +
3100C GLU* 2.9 39.9 + - - +
3101C ALA 3.0 0.6 - - - -
3102C ASP* 1.3 82.6 - - + +
3104C TRP* 1.3 64.7 + - - +
3105C GLU 3.1 2.0 - - - -
3106C HIS* 3.1 21.7 + - - +
3107C VAL* 3.9 10.6 + - - +
4107D VAL* 3.0 48.8 + - + +
4109D SER* 3.6 15.0 - - - +
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Residues in contact with TRP3104 (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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3082C ALA* 4.0 20.9 - - + -
3085C LEU* 3.6 23.6 - - + -
3086C LEU* 3.7 24.2 - - + -
3090C ILE* 4.3 9.9 - - + -
3100C GLU* 2.9 54.3 + - + +
3101C ALA* 3.3 3.8 + - - +
3103C ARG* 1.3 75.9 - - + +
3105C GLU* 1.3 63.5 + - - +
3107C VAL* 2.9 23.5 + - + +
3108C MET* 3.1 19.6 + - + +
4085D LEU* 4.5 6.3 - - + -
4104D TRP* 3.5 43.3 - + + -
4107D VAL* 3.3 25.1 + - + -
4108D MET* 4.4 17.5 - - + -
4112D VAL* 4.2 12.1 - - + -
4116D LEU* 5.6 0.2 - - + -
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Residues in contact with GLU3105 (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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255C NI 1.6 44.6 - - - +
3009C GLU* 4.0 5.5 - - - +
3010C MET* 2.6 3.1 - - - +
3013C ARG* 2.8 25.6 + - - -
3075C VAL* 4.4 14.9 - - + +
3078C LYS* 3.8 34.6 - - - +
3079C HIS* 3.3 29.4 + - + +
3082C ALA* 4.9 0.8 - - - +
3101C ALA 3.0 9.3 + - - +
3102C ASP* 2.3 12.5 - - - +
3104C TRP* 1.3 78.3 - - - +
3106C HIS* 1.3 80.7 + - + +
3107C VAL 3.5 0.9 + - - -
3108C MET* 4.0 1.5 + - - +
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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