Contacts of the strand formed by residues 67 - 75 (chain K) in PDB entry 3HEI
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 ILE 67 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K LEU* 3.8 29.6 - - + -
64K ALA* 3.9 12.6 - - + -
66K ARG* 1.3 77.0 - - - +
68K PHE* 1.3 61.9 + - - +
69K ILE* 4.2 14.0 - - + +
96K TYR* 5.8 1.6 - - + -
142K SER* 3.1 7.8 - - - -
143K VAL* 3.0 52.9 + - + +
146K LEU* 3.7 25.6 - - + -
151K PHE* 3.7 32.8 - - + -
153K LEU* 4.5 3.1 - - + -
169K VAL* 4.0 7.9 - - + -
170K TYR 3.4 5.8 - - - +
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Residues in contact with PHE 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K ARG* 4.1 35.2 - - + -
67K ILE* 1.3 76.9 - - - +
69K ILE* 1.3 62.6 + - - +
140K GLU* 3.8 17.3 - - - -
141K ARG 3.5 3.1 - - - -
142K SER* 3.8 18.4 - - - -
168K ARG 3.5 1.6 - - - +
169K VAL* 3.2 5.4 - - - +
170K TYR* 2.7 64.4 + + + +
171K TYR* 4.5 0.9 - - - -
172K LYS* 3.4 57.4 - - + -
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Residues in contact with ILE 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ILE* 4.2 13.7 - - + +
68K PHE* 1.3 78.1 - - - +
70K GLU* 1.3 60.2 + - - +
71K LEU* 3.7 23.1 + - + +
94K LEU* 4.2 27.7 - - + +
115K ILE* 4.8 3.6 - - + -
139K GLU 3.7 1.4 - - - +
140K GLU* 3.2 6.1 - - - +
141K ARG* 2.8 38.6 + - + +
143K VAL* 4.0 24.7 - - + -
153K LEU* 3.6 46.9 - - + -
167K VAL* 4.7 1.3 - - + -
168K ARG 3.6 2.7 - - - -
169K VAL* 4.4 7.6 - - + +
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PHE 4.1 0.4 - - - -
69K ILE* 1.3 74.8 - - - +
71K LEU* 1.3 64.2 + - - +
72K LYS* 3.6 22.4 + - - +
138K VAL* 3.8 28.3 - - + +
139K GLU 3.5 4.7 - - - +
140K GLU* 3.9 21.3 - - + +
166K SER* 3.7 3.5 + - - +
167K VAL* 3.4 5.0 + - - -
168K ARG* 2.8 69.6 + - + +
170K TYR* 4.8 4.7 - - + -
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ILE* 3.7 20.9 - - + +
70K GLU* 1.3 81.3 - - - +
72K LYS* 1.3 63.7 + - - +
73K PHE* 4.0 10.0 - - + -
92K PHE* 3.9 30.1 - - + -
94K LEU* 4.5 8.5 - - + -
118K ILE* 4.0 23.1 - - + -
137K ASN 3.6 0.3 - - - +
138K VAL* 3.2 7.1 - - - +
139K GLU 2.8 39.5 + - - +
155K PHE* 3.6 31.2 - - + -
164K LEU* 4.1 9.0 - - + -
166K SER 3.3 2.5 - - - -
167K VAL* 4.1 11.4 - - + -
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Residues in contact with LYS 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K GLU* 3.6 25.3 + - - +
71K LEU* 1.3 76.7 - - - +
73K PHE* 1.3 62.0 + - - +
136K LEU* 3.9 31.0 - - + -
137K ASN 3.0 8.1 - - - +
138K VAL* 4.1 21.7 - - + +
164K LEU* 3.7 2.4 - - - +
165K LEU* 2.9 24.8 + - + -
166K SER* 3.0 36.0 + - - +
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Residues in contact with PHE 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K LEU* 4.0 13.9 - - + -
72K LYS* 1.3 77.9 - - - +
74K THR* 1.3 63.1 + - - +
75K VAL* 3.6 30.5 - - + -
92K PHE* 3.7 22.7 - + + -
118K ILE* 3.6 21.1 - - + -
119K ALA 3.8 7.2 - - - -
120K PRO* 3.8 10.3 - - + -
136K LEU* 3.6 6.8 - - - +
137K ASN* 2.8 59.9 + - + -
139K GLU* 3.6 34.8 - - + -
162K VAL* 4.5 1.3 - - + -
163K ALA 3.0 17.7 - - - +
164K LEU* 4.1 9.4 - - + -
165K LEU 4.5 0.4 - - - +
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Residues in contact with THR 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K PHE* 1.3 77.2 - - - +
75K VAL* 1.3 67.2 + - - +
124K THR* 4.2 7.0 - - - +
134K VAL* 4.2 22.0 - - + -
135K LYS 3.6 19.7 - - - +
136K LEU* 4.3 6.7 - - + -
137K ASN* 4.1 4.3 - - - +
162K VAL* 3.4 6.1 - - - +
163K ALA* 2.8 44.8 + - - +
165K LEU* 4.9 1.3 - - + -
113L PRO 3.0 24.5 + - - +
114L PHE* 4.5 10.6 + - + -
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Residues in contact with VAL 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K PHE* 3.6 27.6 - - + -
74K THR* 1.3 80.8 - - - +
76K ARG* 1.3 69.8 + - - +
89K LYS 5.1 1.1 - - - +
90K GLU* 3.6 25.1 - - - +
92K PHE* 5.2 3.6 - - + -
118K ILE 6.0 0.2 - - - +
120K PRO* 3.7 21.1 - - + -
123K ILE* 3.6 19.9 - - + -
124K THR* 2.8 29.8 + - - -
137K ASN* 4.3 3.4 - - - +
161K CYS 3.4 10.1 - - - +
162K VAL* 4.2 14.1 - - + -
113L PRO 5.3 1.1 - - - -
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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
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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