Contacts of the helix formed by residues 3101 - 3115 (chain D) in PDB entry 1G24
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 PRO3101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ASN* 4.7 1.6 - - - +
123A ASN* 5.9 1.6 - - - +
3089D LYS* 4.3 15.0 - - - +
3099D GLY 4.4 2.0 - - - +
3100D PHE* 1.3 90.3 - - + +
3102D SER* 1.3 67.6 + - - +
3103D ASN* 3.3 20.6 - - - +
3104D LEU* 3.0 23.4 + - + -
3105D ILE* 3.0 8.3 + - - +
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Residues in contact with SER3102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS* 2.6 40.3 + - - +
3100D PHE 3.5 1.4 + - - -
3101D PRO* 1.3 71.5 - - - +
3103D ASN* 1.3 62.7 + - - +
3105D ILE* 3.3 3.9 + - - +
3106D LYS* 3.0 30.9 + - - +
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Residues in contact with ASN3103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3101D PRO* 3.6 21.8 - - - +
3102D SER* 1.3 76.3 - - - +
3104D LEU* 1.3 78.8 + - - +
3106D LYS* 3.4 8.5 + - - +
3107D GLN* 3.1 23.0 + - - +
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Residues in contact with LEU3104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3085D GLU* 6.1 1.6 - - + -
3086D ILE* 4.0 25.8 - - + -
3089D LYS* 3.8 30.1 - - + -
3100D PHE* 3.6 30.1 - - + -
3101D PRO* 3.0 22.5 + - + +
3103D ASN* 1.3 81.4 + - - +
3105D ILE* 1.3 61.8 + - - +
3107D GLN* 3.1 25.8 + - - +
3108D VAL* 2.8 38.2 + - + +
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Residues in contact with ILE3105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS* 3.7 23.6 - - - +
3097D ILE* 3.4 33.2 - - + +
3098D ASN* 3.7 15.5 - - - +
3100D PHE* 3.4 22.4 - - + +
3101D PRO 3.0 13.8 + - - +
3102D SER* 3.3 7.6 + - - +
3104D LEU* 1.3 77.4 - - - +
3106D LYS* 1.3 81.2 + - - +
3108D VAL* 3.4 5.4 + - - +
3109D GLU* 3.0 47.7 + - + +
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Residues in contact with LYS3106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS* 5.2 6.3 - - - +
3102D SER* 3.0 20.6 + - - +
3103D ASN* 3.6 10.5 - - - +
3105D ILE* 1.3 99.8 - - - +
3107D GLN* 1.3 56.0 + - - +
3109D GLU* 3.9 13.9 + - + +
3110D LEU* 3.0 40.2 + - + +
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Residues in contact with GLN3107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3075D ALA* 3.3 18.1 + - + +
3078D SER* 2.8 37.9 + - - -
3079D TYR* 3.2 16.3 - - + +
3086D ILE* 3.6 19.7 - - + +
3103D ASN 3.1 13.8 + - - +
3104D LEU* 3.4 26.1 - - + +
3106D LYS* 1.3 74.7 - - - +
3108D VAL* 1.3 63.6 + - + +
3110D LEU* 3.2 9.7 + - - +
3111D LEU* 2.9 30.1 + - + +
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Residues in contact with VAL3108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3086D ILE* 4.5 15.7 - - + -
3090D LEU* 5.0 2.2 - - + -
3097D ILE* 4.0 14.1 - - + -
3100D PHE* 4.6 11.9 - - + -
3104D LEU* 2.8 40.7 + - + +
3105D ILE 3.9 3.1 - - - +
3107D GLN* 1.3 74.7 - - + +
3109D GLU* 1.3 59.2 + - - +
3111D LEU* 3.2 2.4 + - - -
3112D ASP* 2.8 38.8 + - - +
3172D TYR* 3.3 21.5 + - + +
3219D ARG* 3.5 28.5 - - - +
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Residues in contact with GLU3109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3097D ILE* 3.9 23.3 - - + +
3105D ILE* 3.0 31.7 + - - +
3106D LYS* 4.0 14.7 + - + +
3108D VAL* 1.3 75.5 - - - +
3110D LEU* 1.3 62.0 + - + +
3112D ASP* 3.6 9.9 - - - +
3113D LYS* 3.1 25.5 + - - +
3250D PRO* 5.4 0.5 - - - +
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Residues in contact with LEU3110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3071D SER* 3.7 42.4 - - - +
3072D GLU* 4.3 18.3 - - + +
3075D ALA* 3.8 14.6 - - + -
3106D LYS* 3.0 27.8 + - + +
3107D GLN* 3.5 6.3 - - - +
3108D VAL 3.2 0.2 - - - -
3109D GLU* 1.3 75.1 - - - +
3111D LEU* 1.3 64.9 + - - +
3113D LYS* 3.4 4.8 + - + +
3114D SER* 2.9 24.5 + - - -
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Residues in contact with LEU3111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3072D GLU 5.9 0.2 - - - -
3075D ALA* 4.3 7.5 - - + +
3076D ILE* 3.7 27.6 - - + +
3079D TYR* 4.0 26.7 - - + -
3086D ILE* 6.3 0.2 - - + -
3107D GLN* 2.9 18.6 + - + +
3108D VAL* 3.6 4.9 - - - +
3110D LEU* 1.3 77.8 - - - +
3112D ASP* 1.3 62.4 + - - +
3114D SER* 2.6 31.9 + - - +
3115D PHE* 3.2 15.3 - - + -
3118D MET* 5.2 1.1 - - + -
3172D TYR* 3.3 45.8 - - + +
3216D LEU* 4.0 15.5 - - + -
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Residues in contact with ASP3112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3097D ILE* 5.1 0.2 - - - +
3108D VAL* 2.8 28.7 + - - +
3109D GLU* 3.6 10.8 - - - +
3111D LEU* 1.3 75.0 - - - +
3113D LYS* 1.3 60.7 + - - +
3115D PHE* 3.5 22.0 + - - +
3116D ASN* 4.6 2.3 + - - -
3172D TYR* 2.8 24.8 + - - -
3199D LYS* 5.1 0.7 + - - -
3218D PRO* 6.2 0.6 - - - +
3219D ARG* 3.0 35.8 + - - +
3248D ILE* 3.5 28.2 - - + +
3250D PRO* 4.1 14.1 - - + +
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Residues in contact with LYS3113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3072D GLU* 4.4 8.6 - - - +
3109D GLU 3.1 13.6 + - - +
3110D LEU* 4.1 5.2 - - + +
3112D ASP* 1.3 76.3 - - - +
3114D SER* 1.3 66.0 + - - +
3115D PHE 3.0 2.5 - - - -
3116D ASN* 2.9 33.4 + - + +
3117D LYS* 4.4 1.4 + - - +
3250D PRO* 3.8 17.5 - - + -
3251D LYS 3.6 30.8 - - - -
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Residues in contact with SER3114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3068D LEU* 4.5 3.2 - - - +
3072D GLU* 3.6 33.0 + - - -
3076D ILE* 4.5 5.1 - - - +
3110D LEU 2.9 15.6 + - - -
3111D LEU* 2.6 29.0 + - - +
3113D LYS* 1.3 76.6 - - - +
3115D PHE* 1.3 56.7 + - - +
3116D ASN 3.1 0.4 - - - -
3117D LYS* 3.0 22.9 + - - +
3118D MET* 3.2 31.9 + - - +
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Residues in contact with PHE3115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3111D LEU* 3.2 40.6 - - + -
3112D ASP* 3.7 13.0 - - - +
3113D LYS 3.0 1.6 - - - -
3114D SER* 1.3 77.8 + - - +
3116D ASN* 1.3 61.2 + - - +
3117D LYS 2.9 6.7 + - - -
3118D MET* 3.1 26.0 + - + +
3119D LYS* 3.0 18.0 - - - -
3172D TYR* 4.3 4.7 - + - -
3199D LYS* 3.7 34.9 - - + +
3200D ALA 4.0 6.7 - - - -
3201D GLY 4.0 5.8 - - - -
3216D LEU* 3.2 39.3 - - + -
3217D LEU 3.6 7.0 - - - -
3218D PRO* 3.5 39.7 - - + -
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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