Contacts of the strand formed by residues 27 - 32 (chain G) in PDB entry 1NJI
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 GLY 27 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLU* 3.2 2.1 - - - +
24G GLY 2.6 39.5 + - - +
25G ASP 3.4 1.0 - - - -
26G ASN* 1.3 79.6 - - - +
28G SER* 1.3 59.5 + - - -
76G VAL* 3.4 8.5 + - - +
136G PRO* 4.6 6.3 - - - -
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G THR* 4.6 6.3 - - - -
22G VAL 2.9 5.4 - - - -
23G GLU* 3.3 31.6 - - - -
27G GLY* 1.3 73.7 - - - -
29G VAL* 1.3 67.8 + - - +
30G THR* 5.4 0.4 - - - -
76G VAL* 4.2 0.9 - - - +
121G ASP* 5.1 5.5 - - - +
136G PRO* 4.7 6.8 - - - +
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Residues in contact with VAL 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE 3.7 0.9 - - - +
21G THR* 3.1 1.4 - - - -
22G VAL* 2.7 43.2 + - - +
28G SER* 1.3 80.3 - - - +
30G THR* 1.3 70.3 + - - +
31G ARG* 4.3 15.0 - - + -
72G MET* 4.4 20.5 - - + +
76G VAL* 4.4 6.5 - - + -
136G PRO* 3.3 41.3 - - + +
137G ASP* 3.8 29.8 - - + +
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Residues in contact with THR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ASP* 4.3 16.8 - - + +
20G ILE 3.0 15.3 - - - +
21G THR* 3.0 30.4 + - - +
28G SER 4.4 0.7 + - - -
29G VAL* 1.3 76.1 - - - +
31G ARG* 1.3 72.2 + - - +
137G ASP* 5.4 1.4 - - - +
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Residues in contact with ARG 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2793A A 4.4 7.9 + - - -
2794A G 3.7 24.2 + - - -
18G LEU 3.8 0.2 - - - +
19G ASP* 3.2 9.1 - - - +
20G ILE* 2.7 33.8 + - + +
29G VAL* 4.3 8.3 - - + -
30G THR* 1.3 81.2 - - - +
32G ARG* 1.3 69.5 + - - +
33G LEU* 4.0 14.8 + - + +
68G HIS* 2.7 61.7 + - - +
72G MET* 3.6 32.5 - - + -
137G ASP* 6.0 0.7 - - - +
139G GLU* 4.7 23.5 + - - +
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Residues in contact with ARG 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2793A A 6.0 0.9 - - - -
2794A G 5.4 2.4 + - - +
18G LEU* 3.4 25.9 - - + +
19G ASP* 3.6 16.1 + - - +
31G ARG* 1.3 85.6 + - - +
33G LEU* 1.3 70.4 + - - +
34G TRP* 3.4 52.1 + - + +
123K ARG* 4.7 7.9 - - - +
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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