Contacts of the helix formed by residues 3006 - 3021 (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 ASP3006 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3004C LEU 2.5 11.7 + - - -
3005C VAL* 1.3 75.0 - - + +
3007C THR* 1.3 65.8 + - - +
3008C THR* 3.1 16.3 + - - -
3009C GLU* 2.9 45.2 + - - +
3010C MET* 3.3 24.6 + - - +
3106C HIS* 3.8 11.9 - - + +
315E G 5.0 3.1 + - - -
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Residues in contact with THR3007 (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 5.5 2.6 + - - -
3004C LEU* 3.6 14.0 - - + +
3005C VAL 4.1 1.0 - - - -
3006C ASP* 1.3 74.0 + - - +
3008C THR* 1.3 64.1 + - - +
3010C MET* 3.5 1.4 + - - +
3011C TYR* 3.2 31.9 + - + -
3044C THR* 3.8 27.6 - - + +
315E G 3.7 32.7 + - - +
316E C 3.1 35.2 + - - +
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Residues in contact with THR3008 (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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3006C ASP* 3.1 9.1 + - - -
3007C THR* 1.3 77.4 - - - +
3009C GLU* 1.3 68.6 + - + +
3011C TYR* 3.1 15.7 + - - +
3012C LEU* 3.2 20.4 + - + +
3044C THR* 5.6 1.2 - - - +
3048C MET* 4.4 19.7 - - + +
3053C LEU* 3.7 30.1 - - + -
3071C LEU* 5.5 2.0 - - + -
315E G 4.5 12.3 + - - -
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Residues in contact with GLU3009 (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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3006C ASP* 2.9 25.3 + - - +
3007C THR 3.5 0.6 - - - -
3008C THR* 1.3 82.0 - - + +
3010C MET* 1.3 57.4 + - - +
3012C LEU* 3.5 9.3 + - + +
3013C ARG* 3.1 27.2 + - - +
3071C LEU* 6.2 0.9 - - + -
3075C VAL* 4.0 30.3 - - + +
3078C LYS* 6.0 1.6 - - - -
3105C GLU 4.0 3.5 - - - +
3106C HIS* 2.7 61.8 + - + +
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Residues in contact with MET3010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C NI 2.0 39.9 - - + -
3004C LEU* 3.6 30.3 - - + +
3006C ASP 3.3 13.4 + - - +
3007C THR 4.0 3.8 - - - +
3008C THR 3.2 0.8 - - - -
3009C GLU* 1.3 73.8 - - - +
3011C TYR* 1.3 61.0 + - - +
3013C ARG* 3.9 25.5 - - - +
3014C THR* 2.8 34.6 + - - +
3034C LEU* 4.2 16.9 - - + +
3102C ASP* 3.2 17.7 - - - +
3105C GLU* 2.6 4.9 - - - +
3106C HIS* 2.6 15.5 - - + +
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Residues in contact with TYR3011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004C LEU* 4.6 1.1 - - + -
3007C THR* 3.2 31.7 + - + +
3008C THR 3.1 8.1 + - - +
3010C MET* 1.3 74.5 - - - +
3012C LEU* 1.3 67.2 + - - +
3014C THR* 3.2 4.5 + - - -
3015C ILE* 2.9 29.5 + - + +
3030C ILE* 3.8 28.4 - - + +
3034C LEU* 3.3 28.5 - - + -
3036C GLN* 2.8 26.9 + - - -
3041C VAL* 3.3 35.9 - - + +
3044C THR* 3.5 25.3 + - + -
3045C VAL* 4.1 5.4 - - + -
3048C MET* 3.7 29.4 - - + -
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Residues in contact with LEU3012 (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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3008C THR* 3.2 22.9 + - + +
3009C GLU* 3.7 12.6 - - + +
3011C TYR* 1.3 77.1 - - - +
3013C ARG* 1.3 52.6 + - - +
3015C ILE* 2.9 10.1 + - + +
3016C TYR* 2.7 36.7 + - - +
3048C MET* 3.9 19.7 - - + -
3053C LEU* 4.2 11.0 - - + +
3054C VAL* 5.7 0.2 - - + -
3064C MET* 4.5 11.9 - - + +
3068C GLY* 3.8 24.9 - - - +
3071C LEU* 3.4 42.2 - - + -
3072C ALA* 3.8 14.1 - - + +
3075C VAL* 5.1 1.6 - - + -
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Residues in contact with ARG3013 (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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3009C GLU 3.1 14.8 + - - +
3010C MET* 3.9 23.2 - - + +
3012C LEU* 1.3 78.1 - - - +
3014C THR* 1.3 55.0 + - - +
3016C TYR* 3.2 5.9 + - - +
3017C GLU* 2.7 72.6 + - - +
3072C ALA* 4.9 4.4 - - - +
3075C VAL* 4.4 15.5 - - + -
3076C MET* 3.7 32.3 - - + +
3079C HIS* 3.6 15.5 + - - -
3098C HIS* 3.8 18.0 + - - -
3102C ASP* 4.0 7.9 + - - +
3105C GLU* 2.8 44.6 + - - -
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Residues in contact with THR3014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3010C MET* 2.8 25.8 + - - +
3011C TYR* 3.6 6.1 - - - -
3012C LEU 3.2 0.2 - - - -
3013C ARG* 1.3 76.9 + - - +
3015C ILE* 1.3 65.1 + - - +
3017C GLU* 3.9 7.5 - - - +
3018C LEU* 2.8 34.2 + - + +
3030C ILE* 4.3 19.3 - - + -
3033C ARG* 3.7 37.2 + - + +
3034C LEU* 3.4 20.7 - - - +
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Residues in contact with ILE3015 (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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3011C TYR* 2.9 22.9 + - + +
3012C LEU* 3.3 9.0 - - + +
3014C THR* 1.3 76.6 - - - +
3016C TYR* 1.3 65.1 + - - +
3018C LEU* 3.2 9.8 + - - +
3019C GLU* 3.0 30.4 + - - +
3025C PRO* 3.9 19.7 - - + -
3030C ILE* 4.1 10.1 - - + -
3045C VAL* 5.8 1.3 - - + -
3048C MET* 5.1 7.2 - - + -
3054C VAL* 4.2 17.0 - - + -
3062C LEU* 3.4 41.7 - - + +
3064C MET* 3.8 24.9 - - + -
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Residues in contact with TYR3016 (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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3012C LEU 2.7 19.2 + - - +
3013C ARG* 3.5 7.2 - - - +
3015C ILE* 1.3 74.5 - - - +
3017C GLU* 1.3 66.9 + - - +
3019C GLU* 3.0 16.0 + - + +
3020C GLU* 3.2 43.2 + - + +
3064C MET* 3.8 19.7 - - + +
3069C ARG* 4.8 12.3 - - + -
3072C ALA* 4.1 20.2 - - + -
3073C THR* 4.4 21.8 - - + +
3076C MET* 3.6 37.7 - - + +
3080C ARG* 4.6 6.0 + - - -
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Residues in contact with GLU3017 (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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3013C ARG* 2.7 61.1 + - - +
3014C THR* 4.0 6.3 - - - +
3016C TYR* 1.3 76.4 - - + +
3018C LEU* 1.3 61.5 + - - +
3020C GLU* 3.1 20.6 + - - +
3021C GLU* 3.1 28.8 + - - +
3033C ARG* 4.3 11.9 + - - +
3076C MET* 3.7 29.4 - - + +
3079C HIS* 5.0 0.7 - - - -
3098C HIS* 4.7 6.5 + - - -
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Residues in contact with LEU3018 (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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3014C THR* 2.8 35.7 + - + +
3015C ILE* 3.2 9.9 - - - +
3017C GLU* 1.3 78.2 - - - +
3019C GLU* 1.3 60.9 + - - +
3021C GLU* 3.2 10.8 + - - +
3023C VAL* 3.1 60.6 + - + +
3025C PRO* 4.4 13.5 - - + -
3026C LEU 5.1 0.4 - - - +
3029C ARG* 3.4 33.2 - - + -
3030C ILE* 4.8 2.7 - - + +
3033C ARG* 3.2 34.3 - - - +
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Residues in contact with GLU3019 (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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3015C ILE* 3.0 20.0 + - - +
3016C TYR* 3.0 10.4 + - + +
3018C LEU* 1.3 77.8 - - - +
3020C GLU* 1.3 61.9 + - - +
3022C GLY* 3.0 14.5 + - - +
3023C VAL 4.4 3.8 - - - +
3025C PRO* 4.1 18.9 - - + +
3062C LEU 4.1 11.3 - - - +
3063C GLN* 5.5 0.3 - - - -
3064C MET* 3.7 14.8 + - - +
3069C ARG* 2.9 40.9 + - - -
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Residues in contact with GLU3020 (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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3016C TYR* 3.2 44.0 + - + +
3017C GLU* 3.1 16.9 + - - +
3019C GLU* 1.3 77.4 - - - +
3021C GLU* 1.3 62.0 + - + +
3022C GLY 3.2 1.1 + - - -
3076C MET* 5.8 0.2 - - - +
3080C ARG* 3.9 18.1 + - - -
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Residues in contact with GLU3021 (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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3017C GLU* 3.1 22.2 - - - +
3018C LEU* 3.2 8.5 + - - +
3019C GLU 3.2 0.6 - - - -
3020C GLU* 1.3 78.5 - - + +
3022C GLY* 1.3 61.6 + - - +
3023C VAL* 3.5 14.1 + - + +
3033C ARG* 2.6 43.1 + - - -
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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
------------------------------------------------------------
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